[English] 日本語
Yorodumi
- PDB-4hi1: Crystal structure of acylphosphatase C20R mutant from Vibrio chol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hi1
TitleCrystal structure of acylphosphatase C20R mutant from Vibrio cholerae0395
ComponentsAcylphosphatase
KeywordsHYDROLASE / Ferredoxin fold
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity
Similarity search - Function
Acylphosphatase signature 2. / Acylphosphatase / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MOLYBDATE ION / Acylphosphatase
Similarity search - Component
Biological speciesVibrio cholerae O395 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.964 Å
AuthorsNath, S. / Banerjee, R. / Sen, U.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Crystal structure of acylphosphatase C20R mutant from Vibrio cholerae0395
Authors: Nath, S. / Banerjee, R. / Sen, U.
History
DepositionOct 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acylphosphatase
B: Acylphosphatase
C: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6469
Polymers30,8783
Non-polymers7686
Water4,486249
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-46.9 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.710, 81.300, 40.530
Angle α, β, γ (deg.)90.00, 90.52, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Acylphosphatase / Acylphosphate phosphohydrolase


Mass: 10292.619 Da / Num. of mol.: 3 / Mutation: C20R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Strain: ATCC 39541 / Ogawa 395 / O395 / Gene: acyP, VC0395_A0969, VC395_1474 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5F8G9, acylphosphatase
#2: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE


Mass: 159.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: MoO4
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.6M ammonium sulfate, 0.1M bicine pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 13, 2012
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.964→39.708 Å / Num. obs: 17237 / % possible obs: 93.5 %
Reflection shellResolution: 1.96→2.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.062 / Mean I/σ(I) obs: 12.5 / Num. unique all: 17237 / % possible all: 93.5

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BJD

2bjd


Resolution: 1.964→39.708 Å / SU ML: 0.23 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 872 5.07 %RANDOM
Rwork0.1874 ---
obs0.1907 17218 90.52 %-
all-17218 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.964→39.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2045 0 30 249 2324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112131
X-RAY DIFFRACTIONf_angle_d1.3282879
X-RAY DIFFRACTIONf_dihedral_angle_d15.327775
X-RAY DIFFRACTIONf_chiral_restr0.08306
X-RAY DIFFRACTIONf_plane_restr0.005372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9642-2.0220.29011430.21032715X-RAY DIFFRACTION94
2.022-2.08730.29411200.22182028X-RAY DIFFRACTION71
2.0873-2.16190.28291390.20372708X-RAY DIFFRACTION95
2.1619-2.24850.45891340.29582670X-RAY DIFFRACTION94
2.2485-2.35080.3719960.21552108X-RAY DIFFRACTION95
2.3508-2.47470.26081450.20382786X-RAY DIFFRACTION96
2.4747-2.62970.28151380.20322742X-RAY DIFFRACTION97
2.6297-2.83270.28291290.19122522X-RAY DIFFRACTION87
2.8327-3.11770.291510.19472800X-RAY DIFFRACTION98
3.1177-3.56860.23421650.16532609X-RAY DIFFRACTION92
3.5686-4.4950.15651530.14162553X-RAY DIFFRACTION90
4.495-39.71650.18751460.16782839X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 34.199 Å / Origin y: 27.7704 Å / Origin z: 20.3423 Å
111213212223313233
T0.0591 Å2-0.01 Å20.0155 Å2-0.0565 Å20.0039 Å2--0.0754 Å2
L0.6003 °2-0.084 °2-0.0446 °2-0.8396 °20.2407 °2--0.8878 °2
S0.0245 Å °0.0023 Å °0.0485 Å °0.0265 Å °-0.029 Å °0.085 Å °0.0052 Å °-0.0268 Å °0.0012 Å °
Refinement TLS groupSelection details: all

+
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