4Q7Q | pdb_00004q7q

The crystal structure of a possible lipase from Chitinophaga pinensis DSM 2588

PDB DOI: https://doi.org/10.2210/pdb4Q7Q/pdb

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

Deposited: 2014-04-25 Released: 2014-05-14
Deposition Author(s): Tan, K., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.190 (Depositor), 0.189 (DCC)
R-Value Work:
0.153 (Depositor), 0.157 (DCC)
R-Value Observed:
0.155 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of a possible lipase from Chitinophaga pinensis DSM 2588

Tan, K., Tesar, C., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 60.48 kDa
Atom Count: 4,595
Modeled Residue Count: 516
Deposited Residue Count: 532
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipolytic protein G-D-S-L family	A, B	266	Chitinophaga pinensis DSM 2588	Mutation(s): 0 Gene Names: Cpin_6674
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], H [auth B], I [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.190 (Depositor), 0.189 (DCC)
R-Value Work: 0.153 (Depositor), 0.157 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.611	α = 90
b = 80.611	β = 90
c = 93.005	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-05-14

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-05-14
Type: Initial release
Version 1.1: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary