[English] 日本語
Yorodumi
- PDB-1eoi: CRYSTAL STRUCTURE OF ACID PHOSPHATASE FROM ESCHERICHIA BLATTAE CO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eoi
TitleCRYSTAL STRUCTURE OF ACID PHOSPHATASE FROM ESCHERICHIA BLATTAE COMPLEXED WITH THE TRANSITION STATE ANALOG MOLYBDATE
ComponentsACID PHOSPHATASE
KeywordsHYDROLASE / all-alpha
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space
Similarity search - Function
Acid phosphatase, class A, bacterial, conserved site / Class A bacterial acid phosphatases signature. / Acid phosphatase, class A, bacterial / Acid phosphatase homologues / Phosphatidic acid phosphatase type 2/haloperoxidase / Vanadium-containing Chloroperoxidase; domain 1 / Phosphatidic acid phosphatase type 2/haloperoxidase / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
MOLYBDATE ION / Acid phosphatase
Similarity search - Component
Biological speciesEscherichia blattae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsIshikawa, K. / Mihara, Y. / Gondoh, K. / Suzuki, E. / Asano, Y.
CitationJournal: EMBO J. / Year: 2000
Title: X-ray structures of a novel acid phosphatase from Escherichia blattae and its complex with the transition-state analog molybdate.
Authors: Ishikawa, K. / Mihara, Y. / Gondoh, K. / Suzuki, E. / Asano, Y.
History
DepositionMar 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACID PHOSPHATASE
B: ACID PHOSPHATASE
C: ACID PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5796
Polymers75,0993
Non-polymers4803
Water2,252125
1
A: ACID PHOSPHATASE
B: ACID PHOSPHATASE
C: ACID PHOSPHATASE
hetero molecules

A: ACID PHOSPHATASE
B: ACID PHOSPHATASE
C: ACID PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,15812
Polymers150,1996
Non-polymers9606
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area12890 Å2
ΔGint-99 kcal/mol
Surface area46530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.600, 86.600, 205.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a homohexamer. A symmetry partner can be generated from the trimer in the asymmetric unit by the following operation, (1+X-Y, 2-Y, 2/3-Z).

-
Components

#1: Protein ACID PHOSPHATASE /


Mass: 25033.098 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia blattae (bacteria) / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9S1A6, acid phosphatase
#2: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE / Molybdate


Mass: 159.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: MoO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG400, Na2MoO4, Tris, Hepes, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Details: drop contains protein and reservoir solution in a 1:1 ratio
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMHEPES1drop
343-45 %PEG4001reservoir
40.1 MTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 3, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 34578 / Num. obs: 32057 / % possible obs: 89.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 5.3
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.28 / % possible all: 61.6
Reflection shell
*PLUS
% possible obs: 61.6 %

-
Processing

Software
NameVersionClassification
WEISdata scaling
SCALAdata scaling
AMoREphasing
X-PLOR3.851refinement
WEISdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.4→10 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 3095 -RANDOM
Rwork0.212 ---
obs0.218 30944 89.7 %-
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5082 0 15 125 5222
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.585
X-RAY DIFFRACTIONx_torsion_deg24.692
X-RAY DIFFRACTIONx_torsion_impr_deg0.846

+
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