[English] 日本語
Yorodumi
- PDB-1iw8: Crystal Structure of a mutant of acid phosphatase from Escherichi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1iw8
TitleCrystal Structure of a mutant of acid phosphatase from Escherichia blattae (G74D/I153T)
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
Biological speciesEscherichia blattae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsIshikawa, K. / Mihara, Y. / Shimba, N. / Ohtsu, N. / Kawasaki, H. / Suzuki, E. / Asano, Y.
Citation
Journal: PROTEIN ENG. / Year: 2002
Title: Enhancement of nucleoside phosphorylation activity in an acid phosphatase
Authors: Ishikawa, K. / Mihara, Y. / Shimba, N. / Ohtsu, N. / Kawasaki, H. / Suzuki, E. / Asano, Y.
#1: Journal: 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
DepositionApr 22, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: acid phosphatase
B: acid phosphatase
C: acid phosphatase
D: acid phosphatase
E: acid phosphatase
F: acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,05112
Polymers150,4746
Non-polymers5766
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12800 Å2
ΔGint-184 kcal/mol
Surface area49440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.800, 168.200, 58.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
acid phosphatase


Mass: 25079.078 Da / Num. of mol.: 6 / Fragment: residues 1-231 / Mutation: G74D, I153T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia blattae (bacteria) / Plasmid: pUC118 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9S1A6, acid phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: PEG400, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
220 mMTris1droppH8.0
338 %PEG4001reservoir
420 mMTris-HCl1reservoirpH8.4

-
Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 3, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. all: 45889 / Num. obs: 45889 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.084
Reflection shellResolution: 2.5→2.55 Å / % possible all: 91.2
Reflection
*PLUS
Lowest resolution: 10 Å

-
Processing

Software
NameVersionClassification
WEISdata scaling
SCALAdata scaling
AMoREphasing
CNX2000.1refinement
WEISdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D2T

1d2t


Resolution: 2.5→10 Å / Isotropic thermal model: Isotropic / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2298 -RANDOM
Rwork0.243 ---
all0.243 45889 --
obs0.243 45889 97.5 %-
Displacement parametersBiso mean: 36.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9897 0 30 314 10241
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.021
RfactorNum. reflection% reflection
Rfree0.381 335 -
Rwork0.338 --
obs-6867 92.4 %
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 1 / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.31

+
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