4UBP | pdb_00004ubp

STRUCTURE OF BACILLUS PASTEURII UREASE INHIBITED WITH ACETOHYDROXAMIC ACID AT 1.55 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb4UBP/pdb

Classification: HYDROLASE
Organism(s): Sporosarcina pasteurii
Mutation(s): Yes

Deposited: 1999-02-25 Released: 2000-03-06
Deposition Author(s): Benini, S., Rypniewski, W.R., Wilson, K.S., Ciurli, S., Mangani, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.190 (Depositor)
R-Value Work:
0.151 (Depositor)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

The complex of Bacillus pasteurii urease with acetohydroxamate anion from X-ray data at 1.55 A resolution.

Benini, S., Rypniewski, W.R., Wilson, K.S., Miletti, S., Ciurli, S., Mangani, S.

(2000) J Biol Inorg Chem 5: 110-118

PubMed: 10766443 Search on PubMed
DOI: https://doi.org/10.1007/s007750050014
Primary Citation Related Structures:
4UBP

PubMed Abstract:
The structure of Bacillus pasteurii urease inhibited with acetohydroxamic acid was solved and refined anisotropically using synchrotron X-ray cryogenic diffraction data (1.55 A resolution, 99.5% completeness, data redundancy = 26, R-factor = 15.1%, PDB code 4UBP). The two Ni ions in the active site are separated by a distance of 3.53 A. The structure clearly shows the binding mode of the inhibitor anion, symmetrically bridging the two Ni ions in the active site through the hydroxamate oxygen and chelating one Ni ion through the carbonyl oxygen. The flexible flap flanking the active site cavity is in the open conformation. The possible implications of the results on structure-based molecular design of new urease inhibitors are discussed.

Organizational Affiliation

EMBL c/o DESY, Hamburg, Germany.

Macromolecule Content

Total Structure Weight: 87 kDa
Atom Count: 6,809
Modeled Residue Count: 793
Deposited Residue Count: 797
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (UREASE (CHAIN A))	A	101	Sporosarcina pasteurii	Mutation(s): 0 EC: 3.5.1.5
UniProt
Find proteins for P41022 (Sporosarcina pasteurii) Explore P41022 Go to UniProtKB: P41022
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41022
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (UREASE (CHAIN B))	B	126	Sporosarcina pasteurii	Mutation(s): 0 EC: 3.5.1.5
UniProt
Find proteins for P41021 (Sporosarcina pasteurii) Explore P41021 Go to UniProtKB: P41021
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41021
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (UREASE (CHAIN C))	C	570	Sporosarcina pasteurii	Mutation(s): 8 EC: 3.5.1.5
UniProt
Find proteins for P41020 (Sporosarcina pasteurii) Explore P41020 Go to UniProtKB: P41020
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41020
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HAE Query on HAE Download:Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C] mmCIF format, chain F [auth C]	F [auth C]	ACETOHYDROXAMIC ACID C₂ H₅ N O₂ RRUDCFGSUDOHDG-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain D [auth C] SDF format, chain E [auth C] MOL2 format, chain D [auth C] MOL2 format, chain E [auth C] mmCIF format, chain D [auth C] mmCIF format, chain E [auth C]	D [auth C], E [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Focus chain E [auth C] Interactions & Density Focus chain D [auth C] Focus chain E [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	C	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.190 (Depositor)
R-Value Work: 0.151 (Depositor)
R-Value Observed: 0.151 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.88	α = 90
b = 130.88	β = 90
c = 189	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2000-03-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-03-06
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2019-11-06
Changes: Advisory, Data collection, Database references, Derived calculations
Version 1.4: 2023-09-20
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-11-15
Changes: Data collection