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.

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