2WKN | pdb_00002wkn

gamma lactamase from Delftia acidovorans

PDB DOI: https://doi.org/10.2210/pdb2WKN/pdb

Classification: HYDROLASE
Organism(s): Delftia acidovorans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-16 Released: 2010-09-01
Deposition Author(s): Isupov, M.N., Line, K., Gonsalvez, I.S., Gange-Harris, P., Lanzotti, M., Saneei, V., Littlechild, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.269 (Depositor), 0.264 (DCC)
R-Value Work:
0.220 (Depositor), 0.215 (DCC)
R-Value Observed:
0.221 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The Structure of Gamma Lactamase from Delftia Acidovorans

Isupov, M.N., Line, K., Gonsalvez, I.S., Gange-Harris, P., Lanzotti, M., Saneei, V., Littlechild, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 356.78 kDa
Atom Count: 26,920
Modeled Residue Count: 3,264
Deposited Residue Count: 3,272
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FORMAMIDASE	A, B, C, D, E A, B, C, D, E, F, G, H	409	Delftia acidovorans	Mutation(s): 0 EC: 3.5.1.49
UniProt
Find proteins for A9BPK4 (Delftia acidovorans (strain DSM 14801 / SPH-1)) Explore A9BPK4 Go to UniProtKB: A9BPK4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9BPK4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain S [auth F] SDF format, chain T [auth F] SDF format, chain U [auth G] SDF format, chain V [auth G] SDF format, chain W [auth H] SDF format, chain X [auth H] SDF format, chain Q [auth E] SDF format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] MOL2 format, chain U [auth G] MOL2 format, chain V [auth G] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H] MOL2 format, chain Q [auth E] MOL2 format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth F] mmCIF format, chain T [auth F] mmCIF format, chain U [auth G] mmCIF format, chain V [auth G] mmCIF format, chain W [auth H] mmCIF format, chain X [auth H] mmCIF format, chain Q [auth E] mmCIF format, chain L [auth B]	I [auth A] J [auth A] K [auth B] L [auth B] M [auth C] I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth E], R [auth E], S [auth F], T [auth F], U [auth G], V [auth G], W [auth H], X [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.269 (Depositor), 0.264 (DCC)
R-Value Work: 0.220 (Depositor), 0.215 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.871	α = 105.71
b = 94.621	β = 90.27
c = 152.297	γ = 108.46

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-09-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-01
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other, Refinement description