3SQM

Crystal Structure of Glycoside Hydrolase from Synechococcus Complexed with N-acetyl-D-glucosamine

PDB DOI: https://doi.org/10.2210/pdb3SQM/pdb

Classification: HYDROLASE
Organism(s): Picosynechococcus sp. PCC 7002
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-07-05 Released: 2011-07-20
Deposition Author(s): Kim, Y., Chhor, G., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.231
R-Value Work: 0.159
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Glycoside Hydrolase from Synechococcus Complexed with N-acetyl-D-glucosamine

Kim, Y., Chhor, G., Bearden, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 236.55 kDa
Atom Count: 16,306
Modelled Residue Count: 2,068
Deposited Residue Count: 2,140
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 3	A, B, C, D	535	Picosynechococcus sp. PCC 7002	Mutation(s): 0 Gene Names: SYNPCC7002_A0075
UniProt
Find proteins for B1XLD2 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6)) Explore B1XLD2 Go to UniProtKB: B1XLD2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1XLD2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] SDF format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain U [auth D]	E [auth A], I [auth B], N [auth C], U [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain N [auth C] Focus chain U [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain S [auth C] MOL2 format, chain S [auth C]	S [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain S [auth C] Interactions & Density Focus chain S [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain T [auth C] MOL2 format, chain J [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth C]	J [auth B] M [auth B] O [auth C] P [auth C] Q [auth C] J [auth B], M [auth B], O [auth C], P [auth C], Q [auth C], T [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth C] Interactions & Density Focus chain J [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth C]
ACY Query on ACY 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 L [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D]	F [auth A] G [auth A] H [auth A] L [auth B] R [auth C] F [auth A], G [auth A], H [auth A], L [auth B], R [auth C], V [auth D], W [auth D], X [auth D]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.231
R-Value Work: 0.159
R-Value Observed: 0.163
Space Group: P 3₂ 2 1
Diffraction Data: https://doi.org/10.18430/M33SQM

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.139	α = 90
b = 125.139	β = 90
c = 233.745	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
BUCCANEER	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BUCCANEER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-07-20

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2011-07-20
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary