[English] 日本語
Yorodumi
- PDB-3hwk: Crystal structure of methylcitrate synthase from Mycobacterium tu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hwk
TitleCrystal structure of methylcitrate synthase from Mycobacterium tuberculosis
ComponentsMethylcitrate synthase
KeywordsTRANSFERASE / NIAID / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Tubercluosis / UW / SBRI / deCODE / Acyltransferase
Function / homology
Function and homology information


2-methylcitrate synthase / 2-methylcitrate synthase activity / propionate metabolic process, methylcitrate cycle / propionate catabolic process, 2-methylcitrate cycle / citrate synthase activity / citrate synthase (unknown stereospecificity) / : / response to host immune response / response to acidic pH / tricarboxylic acid cycle ...2-methylcitrate synthase / 2-methylcitrate synthase activity / propionate metabolic process, methylcitrate cycle / propionate catabolic process, 2-methylcitrate cycle / citrate synthase activity / citrate synthase (unknown stereospecificity) / : / response to host immune response / response to acidic pH / tricarboxylic acid cycle / carbohydrate metabolic process / cytosol / cytoplasm
Similarity search - Function
2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase ...2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
SUCCINIC ACID / 2-methylcitrate synthase / Citrate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJun 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Methylcitrate synthase
B: Methylcitrate synthase
C: Methylcitrate synthase
D: Methylcitrate synthase
E: Methylcitrate synthase
F: Methylcitrate synthase
G: Methylcitrate synthase
H: Methylcitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,38524
Polymers362,4958
Non-polymers1,88916
Water17,294960
1
A: Methylcitrate synthase
B: Methylcitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3328
Polymers90,6242
Non-polymers7096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-20 kcal/mol
Surface area25740 Å2
MethodPISA
2
C: Methylcitrate synthase
D: Methylcitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0966
Polymers90,6242
Non-polymers4724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9520 Å2
ΔGint-29 kcal/mol
Surface area25990 Å2
MethodPISA
3
E: Methylcitrate synthase
F: Methylcitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9785
Polymers90,6242
Non-polymers3543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-28 kcal/mol
Surface area26270 Å2
MethodPISA
4
G: Methylcitrate synthase
H: Methylcitrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9785
Polymers90,6242
Non-polymers3543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-29 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.580, 179.680, 193.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 6 / Auth seq-ID: 30 - 385 / Label seq-ID: 51 - 406

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH

-
Components

#1: Protein
Methylcitrate synthase / CITRATE SYNTHASE I GLTA1


Mass: 45311.898 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Expressed with an N-terminal hexahis affinity tag and 3C protease cleavage site. Not cleaved prior to crystallization.
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: gltA1, gltA-3, MT1163, Rv1131 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli)
References: UniProt: O08395, UniProt: I6Y9Q3*PLUS, citrate (Si)-synthase
#2: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H6O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 960 / 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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2 M sodium citrate or succinate, 25% glycerol as cryo-protectant, Crystal ID 202737b10, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→19.91 Å / Num. obs: 172140 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.18
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 2.08 / Num. unique all: 12650 / % possible all: 99.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.63 Å19.98 Å
Translation2.63 Å19.98 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A59 with symmetry mate to generate a dimer

1a59


Resolution: 2.3→19.91 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.165 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.851 / SU B: 5.978 / SU ML: 0.145 / SU R Cruickshank DPI: 0.251 / SU Rfree: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.228 8613 5 %RANDOM
Rwork0.186 ---
obs0.188 172140 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.96 Å2 / Biso mean: 34.621 Å2 / Biso min: 12.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2---0.27 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22187 0 128 960 23275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02222831
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.9631005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50452926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59122.37958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.131153597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.85615213
X-RAY DIFFRACTIONr_chiral_restr0.0810.23485
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117492
X-RAY DIFFRACTIONr_mcbond_it0.5711.514562
X-RAY DIFFRACTIONr_mcangle_it1.1223287
X-RAY DIFFRACTIONr_scbond_it1.78738269
X-RAY DIFFRACTIONr_scangle_it2.9484.57714
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2587 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ALOOSE POSITIONAL0.345
BLOOSE POSITIONAL0.315
CLOOSE POSITIONAL0.495
DLOOSE POSITIONAL0.375
ELOOSE POSITIONAL0.295
FLOOSE POSITIONAL0.35
GLOOSE POSITIONAL0.345
HLOOSE POSITIONAL0.35
ALOOSE THERMAL6.6510
BLOOSE THERMAL2.910
CLOOSE THERMAL5.110
DLOOSE THERMAL8.3310
ELOOSE THERMAL5.5410
FLOOSE THERMAL3.0210
GLOOSE THERMAL4.3710
HLOOSE THERMAL9.3910
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 643 -
Rwork0.257 12004 -
all-12647 -
obs--99.78 %

+
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