[English] 日本語
Yorodumi
- PDB-1fwj: KLEBSIELLA AEROGENES UREASE, NATIVE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fwj
TitleKLEBSIELLA AEROGENES UREASE, NATIVE
Components(UREASE) x 3
KeywordsHYDROLASE / HYDROLASE(UREA AMIDO) / NICKEL METALLOENZYME
Function / homology
Function and homology information


urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease, subunit B / Urease, beta subunit / Urease; subunit A / Urease, gamma-like subunit / Urease, gamma subunit / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit ...Urease, subunit B / Urease, beta subunit / Urease; subunit A / Urease, gamma-like subunit / Urease, gamma subunit / Urease active site / Urease active site. / Urease nickel binding site / Urease nickel ligands signature. / Urease, beta subunit / Urease, alpha subunit / Urease alpha subunit, C-terminal / Urease, beta subunit superfamily / Urease beta subunit / Urease domain profile. / Urease alpha-subunit, N-terminal domain / Urease alpha-subunit, N-terminal domain / Urease, gamma/gamma-beta subunit / Urease, gamma subunit superfamily / Urease, gamma subunit / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Ribbon / Roll / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesKlebsiella aerogenes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsPearson, M.A. / Karplus, P.A.
Citation
Journal: Biochemistry / Year: 1997
Title: Structures of Cys319 variants and acetohydroxamate-inhibited Klebsiella aerogenes urease.
Authors: Pearson, M.A. / Michel, L.O. / Hausinger, R.P. / Karplus, P.A.
#1: Journal: Biochemistry / Year: 1996
Title: Structures of the Klebsiella Aerogenes Urease Apoenzyme and Two Active-Site Mutants
Authors: Jabri, E. / Karplus, P.A.
#2: Journal: Science / Year: 1995
Title: The Crystal Structure of Urease from Klebsiella Aerogenes
Authors: Jabri, E. / Carr, M.B. / Hausinger, R.P. / Karplus, P.A.
History
DepositionApr 23, 1997Processing site: BNL
SupersessionOct 15, 1997ID: 1KAU
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UREASE
B: UREASE
C: UREASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3405
Polymers83,2233
Non-polymers1172
Water3,189177
1
A: UREASE
B: UREASE
C: UREASE
hetero molecules

A: UREASE
B: UREASE
C: UREASE
hetero molecules

A: UREASE
B: UREASE
C: UREASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,02015
Polymers249,6689
Non-polymers3526
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area48170 Å2
ΔGint-322 kcal/mol
Surface area55360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)170.800, 170.800, 170.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

-
Components

#1: Protein UREASE / UREA AMIDOHYDROLASE


Mass: 11100.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Plasmid: PKAU19 / Gene (production host): UREA, UREB, UREC / Production host: Klebsiella aerogenes (bacteria) / Strain (production host): CG253 / References: UniProt: P18316, urease
#2: Protein UREASE / UREA AMIDOHYDROLASE


Mass: 11712.239 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Plasmid: PKAU19 / Gene (production host): UREA, UREB, UREC / Production host: Klebsiella aerogenes (bacteria) / Strain (production host): CG253 / References: UniProt: P18315, urease
#3: Protein UREASE / UREA AMIDOHYDROLASE


Mass: 60409.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Plasmid: PKAU19 / Gene (production host): UREA, UREB, UREC / Production host: Klebsiella aerogenes (bacteria) / Strain (production host): CG253 / References: UniProt: P18314, urease
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHREE WATERS, 500, 501, AND 502 ARE LIGATED TO THE ACTIVE SITE NICKEL IONS. THEY MUST BE PARTIALLY ...THREE WATERS, 500, 501, AND 502 ARE LIGATED TO THE ACTIVE SITE NICKEL IONS. THEY MUST BE PARTIALLY OCCUPIED DUE TO CLOSE OXYGEN-OXYGEN DISTANCES BETWEEN THEM.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 49 %
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Jabri, E., (1992) J.Mol.Biol., 227, 934.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlurease1drop
210 mMTris1drop
30.5 mMEDTA1drop
40.5 mMbeta-mercaptoethanol1drop
50.75-0.85 M1dropLi2SO4
650 mMHEPES1drop
71.5-1.7 M1reservoirLi2SO4
8100 mMHEPES1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementRfactor Rwork: 0.173 / Rfactor obs: 0.173 / Highest resolution: 2.2 Å
Details: ALL NON-BONDED INTERACTIONS WERE REMOVED BETWEEN THE ACTIVE SITE NICKEL IONS AND NICKEL-BOUND WATERS 500, 501, 502. THE OCCUPANCIES FOR ACTIVE SITE WATERS HOH 500 - HOH 502 WERE REFINED WITH ...Details: ALL NON-BONDED INTERACTIONS WERE REMOVED BETWEEN THE ACTIVE SITE NICKEL IONS AND NICKEL-BOUND WATERS 500, 501, 502. THE OCCUPANCIES FOR ACTIVE SITE WATERS HOH 500 - HOH 502 WERE REFINED WITH A FIXED B-FACTOR OF 20 ANGSTROMS**2. THE REFINED OCCUPANCIES FOR THESE WATERS SUGGEST NEARLY FULL OCCUPANCY FOR EACH OF THEM, ALTHOUGH THEY ARE POSITIONED TOO CLOSE (~ 2.0 ANGSTROMS APART) FOR SIMULTANEOUS OCCUPANCY. THE OCCUPANCIES FOR ACTIVE SITE WATERS HOH 500 - HOH 502 WERE REFINED WITH A FIXED B-FACTOR OF 20 ANGSTROMS**2. THE REFINED OCCUPANCIES FOR THESE WATERS SUGGEST NEARLY FULL OCCUPANCY FOR EACH OF THEM, ALTHOUGH THEY ARE POSITIONED TOO CLOSE (~ 2.0 ANGSTROMS APART) FOR SIMULTANEOUS OCCUPANCY.
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5789 0 2 177 5968

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more