[English] 日本語
Yorodumi
- PDB-4um4: STRUCTURE OF INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI IN C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4um4
TitleSTRUCTURE OF INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI IN COMPLEX WITH SULFATE
ComponentsINORGANIC PYROPHOSPHATASE
KeywordsHYDROLASE
Function / homology
Function and homology information


inorganic triphosphate phosphatase activity / inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / zinc ion binding / membrane / cytosol
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
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsCampos-Acevedo, A.A. / Rudino-Pinera, E.
CitationJournal: Biochem Biophys Rep / Year: 2016
Title: First attempts to crystallize a non-homogeneous sample of thioredoxin from Litopenaeus vannamei: What to do when you have diffraction data of a protein that is not the target?
Authors: Campos-Acevedo, A.A. / Diaz-Vilchis, A. / Sotelo-Mundo, R.R. / Rudino-Pinera, E.
History
DepositionMay 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Oct 18, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _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: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE
C: INORGANIC PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4746
Polymers59,1863
Non-polymers2883
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-77.1 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.044, 108.943, 81.014
Angle α, β, γ (deg.)90.00, 97.48, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:97 OR RESSEQ 101:173 )
211CHAIN B AND (RESSEQ 1:97 OR RESSEQ 101:173 )
311CHAIN C AND (RESSEQ 1:97 OR RESSEQ 101:173 )

-
Components

#1: Protein INORGANIC PYROPHOSPHATASE / / PYROPHOSPHATE PHOSPHO-HYDROLASE / PPASE


Mass: 19728.529 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7A9, inorganic diphosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 4.44 Å3/Da / Density % sol: 72.28 % / Description: NONE
Crystal growpH: 4.6
Details: 0.1M SODIUM ACETATE TRIHYDRATE, 2.0M AMMONIUM SULFATE,5 MM DTT, pH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.975
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 8, 2011
Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING.
RadiationMonochromator: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.65→19.1 Å / Num. obs: 27508 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 45.79 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.7
Reflection shellResolution: 2.65→2.65 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.4 / % possible all: 94.1

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MJW

1mjw


Resolution: 2.65→19.099 Å / SU ML: 0.34 / σ(F): 1.38 / Phase error: 24.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 1380 5 %
Rwork0.1934 --
obs0.1954 27498 91.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→19.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4143 0 15 74 4232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114427
X-RAY DIFFRACTIONf_angle_d1.3946032
X-RAY DIFFRACTIONf_dihedral_angle_d18.3281689
X-RAY DIFFRACTIONf_chiral_restr0.086662
X-RAY DIFFRACTIONf_plane_restr0.007782
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1317X-RAY DIFFRACTIONPOSITIONAL
12B1317X-RAY DIFFRACTIONPOSITIONAL0.07
13C1293X-RAY DIFFRACTIONPOSITIONAL0.051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.74450.35531360.29642630X-RAY DIFFRACTION94
2.7445-2.8540.31881520.26352699X-RAY DIFFRACTION94
2.854-2.98340.30141300.24392613X-RAY DIFFRACTION93
2.9834-3.14010.28161290.23782695X-RAY DIFFRACTION93
3.1401-3.33590.25211410.20442589X-RAY DIFFRACTION92
3.3359-3.59180.28351310.20592606X-RAY DIFFRACTION92
3.5918-3.95040.23361320.18112630X-RAY DIFFRACTION91
3.9504-4.51550.18031410.15562594X-RAY DIFFRACTION90
4.5155-5.66430.1971360.15252560X-RAY DIFFRACTION90
5.6643-19.09970.19681520.1822502X-RAY DIFFRACTION87

+
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