[English] 日本語
Yorodumi
- PDB-5ts9: Crystal structure of Chorismate mutase from Burkholderia phymatum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ts9
TitleCrystal structure of Chorismate mutase from Burkholderia phymatum
ComponentsChorismate mutase
KeywordsISOMERASE / SSGCID / Chorismate mutase / Burkholderia phymatum / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


chorismate metabolic process / chorismate mutase / chorismate mutase activity
Similarity search - Function
Chorismate mutase, periplasmic / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II ...Chorismate mutase, periplasmic / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesParaburkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of chorismate mutase from Burkholderia phymatum.
Authors: Asojo, O.A. / Subramanian, S. / Abendroth, J. / Exley, I. / Lorimer, D.D. / Edwards, T.E. / Myler, P.J.
History
DepositionOct 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
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 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chorismate mutase
B: Chorismate mutase
C: Chorismate mutase
D: Chorismate mutase
E: Chorismate mutase
F: Chorismate mutase
G: Chorismate mutase
H: Chorismate mutase


Theoretical massNumber of molelcules
Total (without water)150,4018
Polymers150,4018
Non-polymers00
Water23,1311284
1
A: Chorismate mutase
B: Chorismate mutase


Theoretical massNumber of molelcules
Total (without water)37,6002
Polymers37,6002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-6 kcal/mol
Surface area14430 Å2
2
C: Chorismate mutase
D: Chorismate mutase


Theoretical massNumber of molelcules
Total (without water)37,6002
Polymers37,6002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-7 kcal/mol
Surface area14420 Å2
3
E: Chorismate mutase
F: Chorismate mutase


Theoretical massNumber of molelcules
Total (without water)37,6002
Polymers37,6002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-7 kcal/mol
Surface area14610 Å2
4
G: Chorismate mutase
H: Chorismate mutase


Theoretical massNumber of molelcules
Total (without water)37,6002
Polymers37,6002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-7 kcal/mol
Surface area14480 Å2
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13050 Å2
ΔGint-44 kcal/mol
Surface area53270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.590, 151.120, 73.080
Angle α, β, γ (deg.)90.000, 90.840, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Chorismate mutase


Mass: 18800.152 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815) (bacteria)
Strain: DSM 17167 / CIP 108236 / LMG 21445 / STM815 / Gene: Bphy_7813 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2JYH9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1284 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.6 % / Mosaicity: 0.206 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: Microlytic MCSG 1 screen D5: 200mM Ammonium formate pH 6.6, 20% PEG 3350; BuphA.00160.b.B2.PS37873 at 22.4mg/ml; cryo: 10% EG; tray 272085d5, puck LQB7-3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 12, 2016
RadiationMonochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 98259 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.25 % / Biso Wilson estimate: 17.66 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.95-20.5193.010.808199.7
2-2.060.3993.880.896199.5
2.06-2.120.354.340.906199.7
2.12-2.180.2785.320.933199.7
2.18-2.250.2096.740.963199.8
2.25-2.330.1847.660.967199.8
2.33-2.420.1568.610.979199.8
2.42-2.520.13110.080.982199.7
2.52-2.630.11811.150.985199.8
2.63-2.760.10312.40.989199.9
2.76-2.910.09313.640.99199.6
2.91-3.080.08314.840.993199.7
3.08-3.30.07217.040.994199.8
3.3-3.560.05920.430.995199.6
3.56-3.90.05122.820.996199.8
3.9-4.360.04625.190.997199.7
4.36-5.030.04525.360.9961100
5.03-6.170.0522.960.997199.9
6.17-8.720.04525.910.997199.7
8.720.03928.910.997198.3

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4oj7, chain A

4oj7
PDB Unreleased entry


Resolution: 1.95→47.879 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.88
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 2017 2.05 %0
Rwork0.1556 ---
obs0.1566 98234 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.52 Å2 / Biso mean: 21.5348 Å2 / Biso min: 4.1 Å2
Refinement stepCycle: final / Resolution: 1.95→47.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9644 0 0 1295 10939
Biso mean---30.59 -
Num. residues----1295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910273
X-RAY DIFFRACTIONf_angle_d0.92314152
X-RAY DIFFRACTIONf_chiral_restr0.0551687
X-RAY DIFFRACTIONf_plane_restr0.0061916
X-RAY DIFFRACTIONf_dihedral_angle_d13.9166533
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.99880.26021320.199168426974100
1.9988-2.05280.2731690.186367896958100
2.0528-2.11320.25711410.186568767017100
2.1132-2.18150.21371290.165968887017100
2.1815-2.25940.2051510.149568547005100
2.2594-2.34990.18891250.149168716996100
2.3499-2.45680.24071240.153168897013100
2.4568-2.58630.2182980.148969207018100
2.5863-2.74840.19871690.155668537022100
2.7484-2.96060.2021350.165668787013100
2.9606-3.25840.21491800.171268437023100
3.2584-3.72980.20661510.149768947045100
3.7298-4.69850.17891440.128668857029100
4.6985-47.89370.17241690.15046935710499
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)
11.5381-0.20750.36051.47820.5592.1338-0.04150.2156-0.0668-0.2658-0.0085-0.09630.0251-0.03330.02310.1752-0.01710.01860.1953-0.04230.129658.827445.814-2.0796
20.68020.3078-0.24620.98340.45180.9537-0.00180.0829-0.03510.0451-0.0025-0.0070.0154-0.07840.01680.10910.0058-0.00840.1184-0.00890.105251.397856.364615.8313
30.9365-0.1133-0.05870.817-0.10710.4072-0.03450.04120.0488-0.0421-0.0002-0.0671-0.05590.05210.04330.1138-0.0142-0.00390.1016-0.00530.134429.910750.525831.2238
41.9114-0.03210.25531.1009-0.35380.6492-0.0338-0.1817-0.0070.12470.0157-0.07420.0136-0.00720.01790.11880.00110.00340.0989-0.01580.108525.204533.596744.4871
51.0665-0.0593-0.25120.89080.1850.4726-0.0382-0.10120.02960.11020.050.0538-0.01420.0058-0.00510.11240.0050.00440.10740.00740.11954.789516.866544.1908
61.0148-0.3776-0.14220.85820.25130.6356-0.01760.0612-0.0449-0.0575-0.01010.0860.0719-0.06250.03640.1157-0.0221-0.00450.11380.00240.13640.24090.164730.7643
70.91940.2953-0.08960.9661-0.31360.8325-0.04270.0494-0.00990.01510.02490.01270.01920.04210.02660.11460.002-0.00460.1110.00520.0957-21.3442-5.537915.3864
81.84960.2489-0.37641.1642-0.14340.96-0.08830.33570.124-0.2440.0740.0131-0.0668-0.070.01180.1857-0.0262-0.0170.19740.04250.1084-29.04945.2305-2.3875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 181 )A18 - 181
2X-RAY DIFFRACTION2chain 'B' and (resid 21 through 181)B21 - 181
3X-RAY DIFFRACTION3chain 'C' and (resid 20 through 180 )C20 - 180
4X-RAY DIFFRACTION4chain 'D' and (resid 20 through 180 )D20 - 180
5X-RAY DIFFRACTION5chain 'E' and (resid 20 through 180 )E20 - 180
6X-RAY DIFFRACTION6chain 'F' and (resid 19 through 181 )F19 - 181
7X-RAY DIFFRACTION7chain 'G' and (resid 21 through 181 )G21 - 181
8X-RAY DIFFRACTION8chain 'H' and (resid 19 through 181 )H19 - 181

+
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