[English] 日本語
Yorodumi
- PDB-9i2t: Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9i2t
TitleAlpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis
ComponentsAlpha-methylacyl-CoA racemase
KeywordsISOMERASE / CoA-transferase / epimerization / CoA-transferase family III / alpha proton exchange / homodimer
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
: / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III
Similarity search - Domain/homology
ACETATE ION / Alpha-methylacyl-CoA racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMojanaga, O.O. / Acharya, K.R. / Lloyd, M.D.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Molecular basis of acyl-CoA ester recognition by alpha-methylacyl-CoA racemase from Mycobacterium tuberculosis.
Authors: Mojanaga, O.O. / Woodman, T.J. / Lloyd, M.D. / Acharya, K.R.
History
DepositionJan 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-methylacyl-CoA racemase
B: Alpha-methylacyl-CoA racemase
C: Alpha-methylacyl-CoA racemase
D: Alpha-methylacyl-CoA racemase
E: Alpha-methylacyl-CoA racemase
F: Alpha-methylacyl-CoA racemase
G: Alpha-methylacyl-CoA racemase
H: Alpha-methylacyl-CoA racemase
I: Alpha-methylacyl-CoA racemase
J: Alpha-methylacyl-CoA racemase
K: Alpha-methylacyl-CoA racemase
L: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,97523
Polymers468,32612
Non-polymers64911
Water14,232790
1
A: Alpha-methylacyl-CoA racemase
B: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2315
Polymers78,0542
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13150 Å2
ΔGint-81 kcal/mol
Surface area24900 Å2
MethodPISA
2
C: Alpha-methylacyl-CoA racemase
D: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1133
Polymers78,0542
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-79 kcal/mol
Surface area24930 Å2
MethodPISA
3
E: Alpha-methylacyl-CoA racemase
F: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1133
Polymers78,0542
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12780 Å2
ΔGint-78 kcal/mol
Surface area24800 Å2
MethodPISA
4
G: Alpha-methylacyl-CoA racemase
H: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1133
Polymers78,0542
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12640 Å2
ΔGint-80 kcal/mol
Surface area25280 Å2
MethodPISA
5
I: Alpha-methylacyl-CoA racemase
J: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2315
Polymers78,0542
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13230 Å2
ΔGint-82 kcal/mol
Surface area24830 Å2
MethodPISA
6
K: Alpha-methylacyl-CoA racemase
L: Alpha-methylacyl-CoA racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1724
Polymers78,0542
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12920 Å2
ΔGint-83 kcal/mol
Surface area24880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)275.45, 275.45, 388.331
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein
Alpha-methylacyl-CoA racemase / AMACR / MtMCR


Mass: 39027.125 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mcr, Rv1143
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O06543, alpha-methylacyl-CoA racemase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 790 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69.14 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4 M ammonium acetate, 0.1 M Bis-Trispropane, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.953731 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953731 Å / Relative weight: 1
ReflectionResolution: 2.4→224.67 Å / Num. obs: 286594 / % possible obs: 100 % / Redundancy: 27.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.404 / Rpim(I) all: 0.078 / Net I/σ(I): 7.6
Reflection shellResolution: 13.15→224.67 Å / Rmerge(I) obs: 0.062 / Mean I/σ(I) obs: 23.6 / Num. unique obs: 1959 / CC1/2: 0.999 / Rpim(I) all: 0.017 / Rrim(I) all: 0.063 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→224.67 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.376 / SU ML: 0.198 / Cross valid method: FREE R-VALUE / ESU R: 0.251 / ESU R Free: 0.213
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2504 14384 5.019 %
Rwork0.2118 272194 -
all0.214 --
obs-286578 99.994 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 61.541 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å20 Å2
2--0.1 Å20 Å2
3----0.199 Å2
Refinement stepCycle: LAST / Resolution: 2.4→224.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32200 0 44 790 33034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01232989
X-RAY DIFFRACTIONr_bond_other_d0.0010.01631017
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.79844846
X-RAY DIFFRACTIONr_angle_other_deg0.5561.74871155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47854229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.8715312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.613105084
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.21101480
X-RAY DIFFRACTIONr_chiral_restr0.0740.24840
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0240595
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027697
X-RAY DIFFRACTIONr_nbd_refined0.2360.27605
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.230474
X-RAY DIFFRACTIONr_nbtor_refined0.1810.216035
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.217303
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.21389
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0770.224
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0940.22
X-RAY DIFFRACTIONr_nbd_other0.1190.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.060.29
X-RAY DIFFRACTIONr_mcbond_it6.1536.0516999
X-RAY DIFFRACTIONr_mcbond_other6.156.0516998
X-RAY DIFFRACTIONr_mcangle_it9.42910.84221193
X-RAY DIFFRACTIONr_mcangle_other9.4310.84221194
X-RAY DIFFRACTIONr_scbond_it5.246.30815990
X-RAY DIFFRACTIONr_scbond_other5.2386.30715987
X-RAY DIFFRACTIONr_scangle_it8.15211.46123653
X-RAY DIFFRACTIONr_scangle_other8.14911.46123651
X-RAY DIFFRACTIONr_lrange_it11.68453.78837092
X-RAY DIFFRACTIONr_lrange_other11.69353.78137012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.4-2.4620.35210430.353199910.353210360.9060.90499.99050.356
2.462-2.530.34110910.338194200.338205130.9160.91799.99020.34
2.53-2.6030.3359280.31190170.311199470.9220.93399.990.311
2.603-2.6830.3329400.297184280.299193700.9310.94299.98970.294
2.683-2.7710.3199480.288178660.29188140.9330.9451000.283
2.771-2.8680.3218960.27173320.272182290.9360.95499.99450.259
2.868-2.9770.39810.243165160.246174980.9420.96299.99430.228
2.977-3.0980.2818130.235161390.237169550.9510.96599.98230.217
3.098-3.2360.2798480.231154060.233162540.9470.9671000.213
3.236-3.3940.2737550.226147610.228155160.9530.9711000.211
3.394-3.5770.2637260.218140920.22148190.960.97599.99330.205
3.577-3.7940.2327210.203132690.204139900.9680.9791000.192
3.794-4.0560.2196150.188125920.19132070.9730.9821000.181
4.056-4.3810.2035990.171116970.173122960.9760.9831000.166
4.381-4.7990.2125530.169107730.171113270.9730.98399.99120.167
4.799-5.3650.2125330.16497780.166103110.9760.9861000.165
5.365-6.1950.2394400.17686920.17991320.970.9841000.176
6.195-7.5860.2264020.17673690.17977710.9720.9841000.181
7.586-10.7220.1563190.12257680.12460870.9870.9921000.136
10.722-224.670.2312330.2332880.2335240.9670.95299.91490.268

+
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