[English] 日本語
Yorodumi
- PDB-1a5l: K217C VARIANT OF KLEBSIELLA AEROGENES UREASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a5l
TitleK217C VARIANT OF KLEBSIELLA AEROGENES UREASE
Components
  • UREASE (ALPHA SUBUNIT)
  • UREASE (BETA SUBUNIT)
  • UREASE (GAMMA SUBUNIT)
KeywordsHYDROLASE / HYDROLASE (UREA AMIDO) / MUTANT / 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, 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
Urease subunit alpha / Urease subunit beta / Urease subunit gamma
Similarity search - Component
Biological speciesKlebsiella aerogenes (bacteria)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.2 Å
AuthorsPearson, M.A. / Schaller, R.A. / Michel, L.O. / Karplus, P.A. / Hausinger, R.P.
Citation
Journal: Biochemistry / Year: 1998
Title: Chemical rescue of Klebsiella aerogenes urease variants lacking the carbamylated-lysine nickel ligand.
Authors: Pearson, M.A. / Schaller, R.A. / Michel, L.O. / Karplus, P.A. / Hausinger, R.P.
#1: Journal: Acc.Chem.Res. / Year: 1997
Title: 70 Years of Crystalline Urease: What Have We Learned?
Authors: Karplus, P.A. / Pearson, M.A. / Hausinger, R.P.
#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
DepositionFeb 17, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UREASE (GAMMA SUBUNIT)
B: UREASE (BETA SUBUNIT)
C: UREASE (ALPHA SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)82,4363
Polymers82,4363
Non-polymers00
Water3,297183
1
A: UREASE (GAMMA SUBUNIT)
B: UREASE (BETA SUBUNIT)
C: UREASE (ALPHA SUBUNIT)

A: UREASE (GAMMA SUBUNIT)
B: UREASE (BETA SUBUNIT)
C: UREASE (ALPHA SUBUNIT)

A: UREASE (GAMMA SUBUNIT)
B: UREASE (BETA SUBUNIT)
C: UREASE (ALPHA SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)247,3079
Polymers247,3079
Non-polymers00
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area43940 Å2
ΔGint-219 kcal/mol
Surface area56470 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 (GAMMA SUBUNIT)


Mass: 11100.928 Da / Num. of mol.: 1 / Mutation: K217C, C319A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: UREA, UREB, UREC / Plasmid: PKAU17 / Gene (production host): UREA, UREB, UREC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P18316, urease
#2: Protein UREASE (BETA SUBUNIT)


Mass: 11125.690 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: UREA, UREB, UREC / Plasmid: PKAU17 / Gene (production host): UREA, UREB, UREC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P18315, urease
#3: Protein UREASE (ALPHA SUBUNIT)


Mass: 60209.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: UREA, UREB, UREC / Plasmid: PKAU17 / Gene (production host): UREA, UREB, UREC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P18314, urease
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 100 MM HEPES, PH 7.5, 1.6 M LI2SO4
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlurease1drop
210 mMTris-HCl1drop
30.5 mMEDTA1drop
40.5 mMbeta-mercaptoethanol1drop
50.75-0.85 M1dropLi2SO4
650 mMHEPES1drop
71.5-1.7 M1reservoirLi2SO4
8100 mMHEPES1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Oct 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 38169 / % possible obs: 93 % / Redundancy: 2 % / Rsym value: 0.091 / Net I/σ(I): 7.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.288 / % possible all: 69
Reflection
*PLUS
Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 69 % / Rmerge(I) obs: 0.288

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 2.2→10 Å / σ(F): 0
Details: ALL NON-BONDED INTERACTIONS WERE REMOVED BETWEEN THE TWO ALTERNATE CONFORMATIONS OF HIS272 OF CHAIN C THE OCCUPANCIES FOR THE TWO ALTERNATE CONFORMATIONS OBSERVED FOR HIS 272 WERE REFINED ...Details: ALL NON-BONDED INTERACTIONS WERE REMOVED BETWEEN THE TWO ALTERNATE CONFORMATIONS OF HIS272 OF CHAIN C THE OCCUPANCIES FOR THE TWO ALTERNATE CONFORMATIONS OBSERVED FOR HIS 272 WERE REFINED WITH A FIXED B-FACTOR OF 15 (ANGSTROMS)**2.
RfactorNum. reflection% reflection
Rwork0.186 --
obs0.186 37289 99 %
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5542 0 0 183 5725
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.026
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.603
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.06
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.578
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.259 3673 -
obs--71 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.06
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.578
LS refinement shell
*PLUS
Rfactor obs: 0.259

+
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://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