1UBP | pdb_00001ubp

CRYSTAL STRUCTURE OF UREASE FROM BACILLUS PASTEURII INHIBITED WITH BETA-MERCAPTOETHANOL AT 1.65 ANGSTROMS RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb1UBP/pdb

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

Deposited: 1998-01-21 Released: 1999-03-02
Deposition Author(s): Benini, S., Rypniewski, W.R., Wilson, K.S., Ciurli, S., Mangani, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Work:
0.158 (Depositor), 0.172 (DCC)
R-Value Observed:
0.158 (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 beta-mercaptoethanol from X-ray data at 1.65-A resolution

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

(1998) J Biol Inorg Chem 3: 268-273

DOI: https://doi.org/10.1007/s007750050231

Macromolecule Content

Total Structure Weight: 86.65 kDa
Atom Count: 7,077
Modeled Residue Count: 792
Deposited Residue Count: 792
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UREASE	A	100	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
UREASE	B	122	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
UREASE	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
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain G [auth C] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] mmCIF format, chain F [auth C] mmCIF format, chain G [auth C]	F [auth C], G [auth C]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Focus chain G [auth C] Interactions & Density Focus chain F [auth C] Focus chain G [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 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CXM Query on CXM	A	L-PEPTIDE LINKING	C₆ H₁₁ N O₄ S		MET
KCX Query on KCX	C	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Work: 0.158 (Depositor), 0.172 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.343	α = 90
b = 131.343	β = 90
c = 190.013	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 1999-03-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1999-03-02
Type: Initial release
Version 1.1: 2008-03-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2014-04-30
Changes: Database references
Version 1.4: 2019-11-13
Changes: Advisory, Data collection, Database references, Derived calculations
Version 1.5: 2023-08-09
Changes: Advisory, Database references, Derived calculations, Refinement description