4ZXW

Crystal structure of SgcC5 protein from Streptomyces globisporus (complex with (R)-(-)-1-(2-naphthyl)-1,2-ethanediol and sucrose)

PDB DOI: https://doi.org/10.2210/pdb4ZXW/pdb

Classification: LIGASE
Organism(s): Streptomyces globisporus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-05-20 Released: 2015-06-17
Deposition Author(s): Michalska, K., Bigelow, L., Jedrzejczak, R., Babnigg, G., Lohman, J., Ma, M., Rudolf, J., Chang, C.-Y., Shen, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.208
R-Value Work: 0.161
R-Value Observed: 0.162

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of SgcC5 protein from Streptomyces globisporus

Michalska, K., Bigelow, L., Jedrzejczak, R., Babnigg, G., Lohman, J., Ma, M., Rudolf, J., Chang, C.-Y., Shen, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

To be published.

Macromolecule Content

Total Structure Weight: 103.33 kDa
Atom Count: 7,291
Modelled Residue Count: 886
Deposited Residue Count: 924
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-domain type II peptide synthetase	A, B	462	Streptomyces globisporus	Mutation(s): 0
UniProt
Find proteins for Q8GMG2 (Streptomyces globisporus) Explore Q8GMG2 Go to UniProtKB: Q8GMG2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8GMG2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C, D	2		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CXS Query on CXS Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B]	L [auth B]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C₉ H₁₉ N O₃ S PJWWRFATQTVXHA-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
4T7 Query on 4T7 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B]	E [auth A], I [auth B]	(1R)-1-(naphthalen-2-yl)ethane-1,2-diol C₁₂ H₁₂ O₂ QFNOPZNUHSDHKZ-LBPRGKRZSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	F [auth A], G [auth A], H [auth A], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	C, D	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.208
R-Value Work: 0.161
R-Value Observed: 0.162
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M34ZXW

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.397	α = 90
b = 105.304	β = 90
c = 108.167	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-06-17

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM098248

Revision History (Full details and data files)

Version 1.0: 2015-06-17
Type: Initial release
Version 1.1: 2016-09-21
Changes: Source and taxonomy
Version 1.2: 2017-09-06
Changes: Author supporting evidence, Derived calculations
Version 1.3: 2019-12-25
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary

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4ZXW

Crystal structure of SgcC5 protein from Streptomyces globisporus (complex with (R)-(-)-1-(2-naphthyl)-1,2-ethanediol and sucrose)

Crystal structure of SgcC5 protein from Streptomyces globisporus

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2