[English] 日本語
Yorodumi
- PDB-5xo1: Crystal structure of the isochorismatase domain of VabB from Vibr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xo1
TitleCrystal structure of the isochorismatase domain of VabB from Vibrio anguillarum 775
ComponentsIsochorismate lyase
KeywordsHYDROLASE / VabB / isochorismatase / siderophore / iron
Function / homology
Function and homology information


isochorismatase / isochorismatase activity / lyase activity
Similarity search - Function
Isochorismatase / : / Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain ...Isochorismatase / : / Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio anguillarum 775 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsMa, Q. / Du, J.
Funding support China, 4items
OrganizationGrant numberCountry
1000 talents program China
100 talents program, CAS China
aoshan talentsNo. 2015ASTP China
postdoctorial science foundation2015M572091 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2017
Title: Crystal structures of the isochorismatase domains from Vibrio anguillarum.
Authors: Du, J. / Deng, T. / Ma, Q.
History
DepositionMay 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isochorismate lyase
B: Isochorismate lyase
C: Isochorismate lyase
D: Isochorismate lyase
E: Isochorismate lyase
F: Isochorismate lyase


Theoretical massNumber of molelcules
Total (without water)148,6946
Polymers148,6946
Non-polymers00
Water3,153175
1
A: Isochorismate lyase
B: Isochorismate lyase


Theoretical massNumber of molelcules
Total (without water)49,5652
Polymers49,5652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-21 kcal/mol
Surface area16710 Å2
MethodPISA
2
C: Isochorismate lyase
D: Isochorismate lyase


Theoretical massNumber of molelcules
Total (without water)49,5652
Polymers49,5652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-20 kcal/mol
Surface area16570 Å2
MethodPISA
3
E: Isochorismate lyase
F: Isochorismate lyase


Theoretical massNumber of molelcules
Total (without water)49,5652
Polymers49,5652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-21 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.854, 174.005, 49.558
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
Isochorismate lyase


Mass: 24782.371 Da / Num. of mol.: 6 / Fragment: UNP residues 1-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio anguillarum 775 (bacteria) / Strain: 775 / Gene: vabB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5DK16
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 8000, 0.1M imidazole, 0.2M calcium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2016 / Details: dynamically bendable toroidal mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.23→143.85 Å / Num. obs: 61526 / % possible obs: 99.6 % / Redundancy: 14 % / Biso Wilson estimate: 49.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.033 / Rsym value: 0.12 / Net I/σ(I): 14.5
Reflection shellResolution: 2.23→2.238 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.189 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 588 / CC1/2: 0.627 / Rpim(I) all: 0.357 / Rsym value: 1.189 / % possible all: 90.3

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
autoPROC1.0.4data reduction
autoPROC1.0.4data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XO0

5xo0


Resolution: 2.23→32.65 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.939 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.286 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.19
Details: TLS parameters are refined for each chain. Thin shell test set is used.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3058 4.98 %Thin shells
Rwork0.193 ---
obs0.194 61425 99.5 %-
Displacement parametersBiso mean: 58.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.1086 Å20 Å20 Å2
2---5.7917 Å20 Å2
3---3.6831 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.23→32.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9757 0 0 175 9932
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110004HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0913623HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3402SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes250HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1415HARMONIC5
X-RAY DIFFRACTIONt_it10004HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion19.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1346SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11449SEMIHARMONIC4
LS refinement shellResolution: 2.23→2.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.224 4246 -
all0.224 4246 -
obs--94.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.997-0.60590.65732.4176-0.32351.05310.1007-0.0634-0.20140.037-0.02020.19220.0728-0.0157-0.0805-0.18390.0887-0.0141-0.12460.0108-0.059352.73686.589670.2958
23.5556-0.81660.38582.6997-0.856520.11460.4580.7695-0.03-0.3707-0.5671-0.16680.29950.2561-0.24540.07020.0498-0.19670.1490.080368.51526.834560.2346
32.1256-0.3489-0.26212.0899-0.30781.6235-0.0098-0.1912-0.15340.08990.09010.206-0.1951-0.2184-0.0802-0.15410.0824-0.0114-0.03990.0267-0.152513.395133.686964.6892
43.083-1.50650.80682.2246-0.27032.15340.45150.527-0.9009-0.4548-0.19530.51230.33780.1113-0.2563-0.13210.1456-0.1931-0.1247-0.1460.011823.808312.341750.4599
52.5824-0.30480.70791.5716-0.56161.4972-0.06010.20030.3338-0.21510.0048-0.0385-0.14430.1140.0553-0.103-0.0054-0.0095-0.07840.0183-0.145930.713259.94648.2174
63.36090.0393-0.30531.80670.12072.8283-0.0305-0.2140.4864-0.0490.0207-0.5492-0.10610.70320.0097-0.3336-0.0213-0.01330.0422-0.0413-0.025454.343159.305862.665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

+
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