[English] 日本語
Yorodumi
- PDB-1x74: Alpha-methylacyl-CoA racemase from Mycobacterium tuberculosis- mu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1x74
TitleAlpha-methylacyl-CoA racemase from Mycobacterium tuberculosis- mutational and structural characterization of the fold and active site
Components2-methylacyl-CoA racemase
KeywordsISOMERASE / Alpha-methylacyl-CoA racemase / racemase / CoA transferase / Coenzyme A
Function / homology
Function and homology information


alpha-methylacyl-CoA racemase / alpha-methylacyl-CoA racemase activity / acyl-CoA metabolic process / lipid metabolic process / protein homodimerization activity
Similarity search - Function
Wheat Germ Agglutinin (Isolectin 2); domain 1 - #110 / Helix Hairpins - #330 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #260 / : / formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily ...Wheat Germ Agglutinin (Isolectin 2); domain 1 - #110 / Helix Hairpins - #330 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #260 / : / formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Alpha-methylacyl-CoA racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.79 Å
AuthorsKalle, S. / Bhaumik, P. / Schmitz, W. / Kotti, T.J. / Conzelmann, E. / Wierenga, R.K. / Hiltunen, J.K.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: {alpha}-Methylacyl-CoA Racemase from Mycobacterium tuberculosis: MUTATIONAL AND STRUCTURAL CHARACTERIZATION OF THE ACTIVE SITE AND THE FOLD
Authors: Savolainen, K. / Bhaumik, P. / Schmitz, W. / Kotti, T.J. / Conzelmann, E. / Wierenga, R.K. / Hiltunen, J.K.
History
DepositionAug 13, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 13, 2024Group: 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 / diffrn_source / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: 2-methylacyl-CoA racemase
B: 2-methylacyl-CoA racemase
C: 2-methylacyl-CoA racemase
D: 2-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,36820
Polymers154,8914
Non-polymers1,47616
Water26,2661458
1
A: 2-methylacyl-CoA racemase
B: 2-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0909
Polymers77,4462
Non-polymers6457
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14390 Å2
ΔGint-96 kcal/mol
Surface area24880 Å2
MethodPISA
2
C: 2-methylacyl-CoA racemase
D: 2-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,27711
Polymers77,4462
Non-polymers8329
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14560 Å2
ΔGint-93 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.073, 79.779, 117.619
Angle α, β, γ (deg.)90.00, 92.04, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAPROPROAA2 - 392 - 39
21ALAALAPROPROBB2 - 392 - 39
31ALAALAPROPROCC2 - 392 - 39
41ALAALAPROPRODD2 - 392 - 39
52ILEILEALAALAAA45 - 28045 - 280
62ILEILEALAALABB45 - 28045 - 280
72ILEILEALAALACC45 - 28045 - 280
82ILEILEALAALADD45 - 28045 - 280
93SERSERGLUGLUAA294 - 321294 - 321
103SERSERGLUGLUBB294 - 321294 - 321
113SERSERGLUGLUCC294 - 321294 - 321
123SERSERGLUGLUDD294 - 321294 - 321
134TRPTRPGLYGLYAA326 - 360326 - 360
144TRPTRPGLYGLYBB326 - 360326 - 360
154TRPTRPGLYGLYCC326 - 360326 - 360
164TRPTRPGLYGLYDD326 - 360326 - 360

-
Components

#1: Protein
2-methylacyl-CoA racemase / Alpha-methylacyl-CoA racemase


Mass: 38722.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O06543, alpha-methylacyl-CoA racemase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1458 / 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: 2.6 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: Ammonium phosphate, pH 7.0, VAPOR DIFFUSION, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8112 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 2, 2003 / Details: Bent mirror
RadiationMonochromator: Triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8112 Å / Relative weight: 1
ReflectionResolution: 1.79→35 Å / Num. all: 155993 / Num. obs: 155993 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.05 / Net I/σ(I): 16.5
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.4 / Num. unique all: 15483 / Rsym value: 0.315 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.79→19.96 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.181 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.104 / ESU R Free: 0.102
RfactorNum. reflection% reflectionSelection details
Rfree0.19333 7398 5 %RANDOM
Rwork0.16047 ---
obs0.16215 147970 99.47 %-
all-147970 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.451 Å2
Refinement stepCycle: LAST / Resolution: 1.79→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10716 0 95 1458 12269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02111220
X-RAY DIFFRACTIONr_angle_refined_deg1.131.95815234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.49851425
X-RAY DIFFRACTIONr_chiral_restr0.1050.21628
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028740
X-RAY DIFFRACTIONr_nbd_refined0.2020.25644
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.21253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.295
X-RAY DIFFRACTIONr_mcbond_it0.7031.57069
X-RAY DIFFRACTIONr_mcangle_it1.198211271
X-RAY DIFFRACTIONr_scbond_it2.02334151
X-RAY DIFFRACTIONr_scangle_it3.1324.53963
Refine LS restraints NCS

Ens-ID: 1 / Number: 2556 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.145
2Bloose positional0.145
3Cloose positional0.215
4Dloose positional0.195
1Aloose thermal0.7610
2Bloose thermal0.8710
3Cloose thermal0.9110
4Dloose thermal0.9510
LS refinement shellResolution: 1.79→1.886 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.259 1157 -
Rwork0.22 20676 -
obs-15483 99.9 %

+
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