4DYK | pdb_00004dyk

Crystal structure of an adenosine deaminase from pseudomonas aeruginosa pao1 (target nysgrc-200449) with bound zn

PDB DOI: https://doi.org/10.2210/pdb4DYK/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-02-29 Released: 2012-03-14
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Sojitra, S., Chamala, S., Kar, A., Lafleur, J., Villigas, G., Evans, B., Hammonds, J., Gizzi, A., Zencheck, W.D., Hillerich, B., Love, J., Seidel, R.D., Bonanno, J.B., Raushel, F.M., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.224 (Depositor), 0.218 (DCC)
R-Value Work:
0.176 (Depositor), 0.172 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of an adenosine deaminase from pseudomonas aeruginosa pao1 (target nysgrc-200449) with bound zn

Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Sojitra, S., Chamala, S., Kar, A., Lafleur, J., Villigas, G., Evans, B., Hammonds, J., Gizzi, A., Zencheck, W.D., Hillerich, B., Love, J., Seidel, R.D., Bonanno, J.B., Raushel, F.M., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Macromolecule Content

Total Structure Weight: 99.29 kDa
Atom Count: 7,035
Modeled Residue Count: 874
Deposited Residue Count: 902
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMIDOHYDROLASE	A, B	451	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: PA3170
UniProt
Find proteins for Q9HZ64 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HZ64 Go to UniProtKB: Q9HZ64
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HZ64
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 I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.224 (Depositor), 0.218 (DCC)
R-Value Work: 0.176 (Depositor), 0.172 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.906	α = 90
b = 98.776	β = 90
c = 119.82	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-03-14

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2012-03-14
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description