4Q52 | pdb_00004q52

2.60 Angstrom resolution crystal structure of a conserved uncharacterized protein from Chitinophaga pinensis DSM 2588

PDB DOI: https://doi.org/10.2210/pdb4Q52/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Chitinophaga pinensis DSM 2588
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-04-15 Released: 2014-05-07
Deposition Author(s): Halavaty, A.S., Filippova, E.V., Wawrzak, Z., Kiryukhina, O., Minasov, G., Jedrzejczak, R., Shuvalova, L., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.215 (Depositor), 0.216 (DCC)
R-Value Work:
0.169 (Depositor), 0.176 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

2.60 Angstrom resolution crystal structure of a conserved uncharacterized protein from Chitinophaga pinensis DSM 2588

Halavaty, A.S., Filippova, E.V., Wawrzak, Z., Kiryukhina, O., Minasov, G., Jedrzejczak, R., Shuvalova, L., Joachimiak, A., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 83.03 kDa
Atom Count: 5,573
Modeled Residue Count: 687
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D	184	Chitinophaga pinensis DSM 2588	Mutation(s): 0 Gene Names: Cpin_5099

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth D] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth D] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth D]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [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: 2.60 Å
R-Value Free: 0.215 (Depositor), 0.216 (DCC)
R-Value Work: 0.169 (Depositor), 0.176 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.712	α = 90
b = 85.549	β = 104.19
c = 88.195	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-05-07

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-05-07
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Refinement description, Structure summary