4I6V | pdb_00004i6v

The crystal structure of an amidohydrolase 2 from Planctomyces limnophilus DSM 3776

PDB DOI: https://doi.org/10.2210/pdb4I6V/pdb

Classification: HYDROLASE
Organism(s): Planctopirus limnophila DSM 3776
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-11-30 Released: 2013-02-06
Deposition Author(s): Fan, Y., Tan, K., Wu, R., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.218 (Depositor), 0.212 (DCC)
R-Value Work:
0.168 (Depositor), 0.165 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of an amidohydrolase 2 from Planctomyces limnophilus DSM 3776

Fan, Y., Tan, K., Wu, R., Bearden, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 150.96 kDa
Atom Count: 10,812
Modeled Residue Count: 1,280
Deposited Residue Count: 1,302
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidohydrolase 2	A, B, C	434	Planctopirus limnophila DSM 3776	Mutation(s): 0 Gene Names: Planctomyces limnophilus, Plim_2160
UniProt
Find proteins for D5SMT1 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5SMT1 Go to UniProtKB: D5SMT1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D5SMT1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	E [auth A] F [auth A] J [auth B] K [auth B] L [auth B] E [auth A], F [auth A], J [auth B], K [auth B], L [auth B], M [auth B], O [auth C], P [auth C], Q [auth C], R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain N [auth C] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B], N [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain N [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.218 (Depositor), 0.212 (DCC)
R-Value Work: 0.168 (Depositor), 0.165 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.224	α = 90
b = 111.245	β = 90
c = 147.148	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: 2013-02-06

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-02-06
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary