[English] 日本語
Yorodumi
- PDB-8bv9: Acylphosphatase from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bv9
TitleAcylphosphatase from E. coli
ComponentsAcylphosphatase
KeywordsHYDROLASE / ALPHA AND BETA PROTEINS / AMYLOID / PHOSPHATASE / Intertwined
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity
Similarity search - Function
Acylphosphatase, bacteria / Acylphosphatase signature 2. / Acylphosphatase / Acylphosphatase signature 1. / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsGavira, J.A. / Martinez-Rodriguez, S.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-116261GB-I00 Spain
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: First 3-D structural evidence of a native-like intertwined dimer in the acylphosphatase family.
Authors: Martinez-Rodriguez, S. / Camara-Artigas, A. / Gavira, J.A.
History
DepositionJan 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7946
Polymers11,3861
Non-polymers4085
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-22 kcal/mol
Surface area6520 Å2
Unit cell
Length a, b, c (Å)40.415, 81.944, 63.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

-
Components

#1: Protein Acylphosphatase / Acylphosphate phosphohydrolase


Mass: 11385.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yccX, Z1320, ECs1052 / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AB66, acylphosphatase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.4 % / Description: Neddle
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M AS 30% w/v PEG4K / PH range: 4.0-9.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 18, 2021
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.55→41.01 Å / Num. obs: 3631 / % possible obs: 99 % / Redundancy: 6.5 % / Biso Wilson estimate: 68.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.053 / Rrim(I) all: 0.109 / Net I/σ(I): 10.2
Reflection shellResolution: 2.55→2.67 Å / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 431 / CC1/2: 0.44

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→41.01 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 33.59 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.30077 389 10.7 %RANDOM
Rwork0.23266 ---
obs0.23894 3241 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.588 Å2
Baniso -1Baniso -2Baniso -3
1-2.68 Å20 Å2-0 Å2
2--0.19 Å20 Å2
3----2.86 Å2
Refinement stepCycle: LAST / Resolution: 2.55→41.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms732 0 24 8 764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.017820
X-RAY DIFFRACTIONr_bond_other_d0.0010.019789
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.8641107
X-RAY DIFFRACTIONr_angle_other_deg1.0772.5671812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2845104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.67318.84652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.73915147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6581512
X-RAY DIFFRACTIONr_chiral_restr0.10.2113
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02923
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02209
X-RAY DIFFRACTIONr_mcbond_it1.2023.16389
X-RAY DIFFRACTIONr_mcbond_other1.2033.16388
X-RAY DIFFRACTIONr_mcangle_it2.0294.734490
X-RAY DIFFRACTIONr_mcangle_other2.0274.734491
X-RAY DIFFRACTIONr_scbond_it1.4733.599429
X-RAY DIFFRACTIONr_scbond_other1.4323.445423
X-RAY DIFFRACTIONr_scangle_other2.2745.073602
X-RAY DIFFRACTIONr_long_range_B_refined7.15135.689861
X-RAY DIFFRACTIONr_long_range_B_other7.15235.652861
LS refinement shellResolution: 2.551→2.618 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.53 26 -
Rwork0.351 229 -
obs--99.22 %
Refinement TLS params.Method: refined / Origin x: -0.822 Å / Origin y: 17.127 Å / Origin z: 15.735 Å
111213212223313233
T0.0241 Å2-0.0273 Å2-0.0518 Å2-0.4115 Å20.0256 Å2--0.4473 Å2
L4.3728 °2-1.3815 °2-1.5344 °2-4.5875 °2-0.3555 °2--5.8717 °2
S-0.0778 Å °-0.462 Å °0.1094 Å °-0.0311 Å °0.1309 Å °-0.0653 Å °-0.24 Å °0.398 Å °-0.0531 Å °

+
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