[English] 日本語
Yorodumi
- PDB-6ki7: Pyrophosphatase mutant K30R from Acinetobacter baumannii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ki7
TitlePyrophosphatase mutant K30R from Acinetobacter baumannii
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / Pyrophosphatase / mutant K30R
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Inorganic Pyrophosphatase / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Inorganic pyrophosphatase / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSu, J.
CitationJournal: Int J Mol Sci / Year: 2019
Title: Crystal Structures of Pyrophosphatase from Acinetobacter baumannii: Snapshots of Pyrophosphate Binding and Identification of a Phosphorylated Enzyme Intermediate.
Authors: Si, Y. / Wang, X. / Yang, G. / Yang, T. / Li, Y. / Ayala, G.J. / Li, X. / Wang, H. / Su, J.
History
DepositionJul 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase
D: Inorganic pyrophosphatase
E: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase
G: Inorganic pyrophosphatase
H: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)156,2498
Polymers156,2498
Non-polymers00
Water41423
1
A: Inorganic pyrophosphatase

A: Inorganic pyrophosphatase

A: Inorganic pyrophosphatase

E: Inorganic pyrophosphatase

E: Inorganic pyrophosphatase

E: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)117,1876
Polymers117,1876
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation4_565y,x+1,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_455-x-1,-x+y,-z1
Buried area13280 Å2
ΔGint-111 kcal/mol
Surface area39220 Å2
MethodPISA
2
B: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase

B: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase

B: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)117,1876
Polymers117,1876
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area13460 Å2
ΔGint-109 kcal/mol
Surface area38770 Å2
MethodPISA
3
C: Inorganic pyrophosphatase
H: Inorganic pyrophosphatase

C: Inorganic pyrophosphatase
H: Inorganic pyrophosphatase

C: Inorganic pyrophosphatase
H: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)117,1876
Polymers117,1876
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area13180 Å2
ΔGint-114 kcal/mol
Surface area39040 Å2
MethodPISA
4
D: Inorganic pyrophosphatase
x 6


Theoretical massNumber of molelcules
Total (without water)117,1876
Polymers117,1876
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area13070 Å2
ΔGint-112 kcal/mol
Surface area40750 Å2
MethodPISA
5
G: Inorganic pyrophosphatase

G: Inorganic pyrophosphatase

G: Inorganic pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)58,5933
Polymers58,5933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area3820 Å2
ΔGint-31 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.049, 113.049, 551.802
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein
Inorganic pyrophosphatase / / Pyrophosphate phospho-hydrolase / PPase


Mass: 19531.154 Da / Num. of mol.: 8 / Mutation: K30R/A139S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ppa / Production host: Escherichia coli (E. coli)
References: UniProt: N9S5K0, UniProt: A0A333SMX2*PLUS, inorganic diphosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Source detailsThe protein was from a strain of Acinetobacter baumannii from a hospital. The sequence reference ...The protein was from a strain of Acinetobacter baumannii from a hospital. The sequence reference used is from a different species Acinetobacter ursingii NIPH 706.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / Details: salt

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.75→19.96 Å / Num. obs: 35879 / % possible obs: 99.6 % / Redundancy: 9.8 % / Net I/σ(I): 7.6
Reflection shellResolution: 2.75→2.88 Å / Num. unique obs: 4703

-
Processing

SoftwareName: PHENIX / Version: 1.12_2829 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→19.96 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 41.96
RfactorNum. reflection% reflection
Rfree0.3244 1978 5.6 %
Rwork0.2916 --
obs0.2934 35352 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 252.3 Å2 / Biso mean: 74.7893 Å2 / Biso min: 16.59 Å2
Refinement stepCycle: final / Resolution: 2.75→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10781 0 0 23 10804
Biso mean---74.79 -
Num. residues----1384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411061
X-RAY DIFFRACTIONf_angle_d0.715085
X-RAY DIFFRACTIONf_chiral_restr0.0491656
X-RAY DIFFRACTIONf_plane_restr0.0051976
X-RAY DIFFRACTIONf_dihedral_angle_d6.8766677
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.75-2.81860.41091400.38752371100
2.8186-2.89460.32751410.32022387100
2.8946-2.97950.34241400.3178235099
2.9795-3.07540.3661400.3251237599
3.0754-3.18490.36691390.3169237199
3.1849-3.31180.32661420.3086240099
3.3118-3.46180.34871400.295236799
3.4618-3.64330.28141430.2899240599
3.6433-3.870.29961400.2787236399
3.87-4.16630.3661430.2642241299
4.1663-4.5810.27071420.2585237898
4.581-5.23340.34111450.2542243199
5.2334-6.55450.37431440.293244198
6.5545-19.960.27491390.3219232390

+
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