4DLF | pdb_00004dlf

Crystal structure of an amidohydrolase (COG3618) from burkholderia multivorans (TARGET EFI-500235) with bound ZN, space group P3221

PDB DOI: https://doi.org/10.2210/pdb4DLF/pdb

Classification: HYDROLASE
Organism(s): Burkholderia multivorans ATCC 17616
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-02-06 Released: 2012-02-29
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Seidel, R.D., Hillerich, B., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Al Obaidi, N.F., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Raushel, F.M., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.228 (Depositor), 0.219 (DCC)
R-Value Work:
0.193 (Depositor), 0.189 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of an amidohydrolase (COG3618) from burkholderia multivorans (target efi-500235) with bound ZN, space group P3221

Vetting, M.W., Toro, R., Bhosle, R., Seidel, R.D., Hillerich, B., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Al Obaidi, N.F., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Raushel, F.M., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 34.31 kDa
Atom Count: 2,546
Modeled Residue Count: 287
Deposited Residue Count: 303
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidohydrolase 2	A	303	Burkholderia multivorans ATCC 17616	Mutation(s): 0 Gene Names: Bmul_3602, BMULJ_04915 EC: 3.1.1.120
UniProt
Find proteins for A0A0H3KNC4 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore A0A0H3KNC4 Go to UniProtKB: A0A0H3KNC4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3KNC4
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 F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	G [auth A], H [auth A], I [auth A], J [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.228 (Depositor), 0.219 (DCC)
R-Value Work: 0.193 (Depositor), 0.189 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.3	α = 90
b = 75.3	β = 90
c = 142.45	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-02-29

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-02-29
Type: Initial release
Version 1.1: 2018-01-31
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description