[English] 日本語
Yorodumi
- PDB-3bic: Crystal structure of human methylmalonyl-CoA mutase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bic
TitleCrystal structure of human methylmalonyl-CoA mutase
ComponentsMethylmalonyl-CoA mutase, mitochondrial precursor
KeywordsISOMERASE / organic aciduria / methylmalonyl CoA mutase deficiency / metabolic disease / Structural Genomics / Structural Genomics Consortium / SGC / Cobalamin / Cobalt / Disease mutation / Metal-binding / Mitochondrion / Transit peptide
Function / homology
Function and homology information


succinyl-CoA biosynthetic process / Defective MMAA causes MMA, cblA type / Defective MUT causes MMAM / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / Propionyl-CoA catabolism / Cobalamin (Cbl) metabolism / methylmalonyl-CoA mutase activity / modified amino acid binding / homocysteine metabolic process ...succinyl-CoA biosynthetic process / Defective MMAA causes MMA, cblA type / Defective MUT causes MMAM / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / Propionyl-CoA catabolism / Cobalamin (Cbl) metabolism / methylmalonyl-CoA mutase activity / modified amino acid binding / homocysteine metabolic process / cobalamin binding / post-embryonic development / positive regulation of GTPase activity / mitochondrial matrix / GTPase activity / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Methylmalonyl-CoA mutase signature. / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, alpha chain, catalytic / Methylmalonyl-CoA mutase, alpha/beta chain, catalytic / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, C-terminal / Cobalamin-binding domain / Cobalamin (vitamin B12)-dependent enzyme, catalytic / B12 binding domain / Cobalamin-binding domain superfamily ...Methylmalonyl-CoA mutase signature. / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, alpha chain, catalytic / Methylmalonyl-CoA mutase, alpha/beta chain, catalytic / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, C-terminal / Cobalamin-binding domain / Cobalamin (vitamin B12)-dependent enzyme, catalytic / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Methylmalonyl-CoA mutase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsUgochukwu, E. / Kochan, G. / Pantic, N. / Parizotto, E. / Pilka, E.S. / Pike, A.C.W. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. ...Ugochukwu, E. / Kochan, G. / Pantic, N. / Parizotto, E. / Pilka, E.S. / Pike, A.C.W. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structures of the human GTPase MMAA and vitamin B12-dependent methylmalonyl-CoA mutase and insight into their complex formation.
Authors: Froese, D.S. / Kochan, G. / Muniz, J.R. / Wu, X. / Gileadi, C. / Ugochukwu, E. / Krysztofinska, E. / Gravel, R.A. / Oppermann, U. / Yue, W.W.
History
DepositionNov 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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.end_auth_comp_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: Methylmalonyl-CoA mutase, mitochondrial precursor
B: Methylmalonyl-CoA mutase, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,8136
Polymers169,6722
Non-polymers1424
Water1,51384
1
A: Methylmalonyl-CoA mutase, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9073
Polymers84,8361
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methylmalonyl-CoA mutase, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9073
Polymers84,8361
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.750, 95.150, 119.160
Angle α, β, γ (deg.)90.00, 108.31, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
12A
22B
32A
42B
52A
62B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROTRPTRP2AA38 - 32928 - 319
211PROPROTRPTRP2BB38 - 32928 - 319
321ILEILESERSER2AA333 - 594323 - 584
421ILEILESERSER2BB333 - 594323 - 584
531PROPROTHRTHR2AA615 - 673605 - 663
631PROPROTHRTHR2BB615 - 673605 - 663
741HISHISLYSLYS2AA678 - 745668 - 735
841HISHISLYSLYS2BB678 - 745668 - 735
112ALAALALEULEU6AA330 - 332320 - 322
212ALAALALEULEU6BB330 - 332320 - 322
322LYSLYSARGARG6AA595 - 614585 - 604
422LYSLYSARGARG6BB595 - 614585 - 604
532LEULEUGLYGLY6AA674 - 677664 - 667
632LEULEUGLYGLY6BB674 - 677664 - 667

NCS ensembles :
ID
1
2

-
Components

#1: Protein Methylmalonyl-CoA mutase, mitochondrial precursor / MCM / Methylmalonyl-CoA isomerase


Mass: 84835.820 Da / Num. of mol.: 2 / Fragment: Residues 12-750
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUT / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: P22033, methylmalonyl-CoA mutase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.29 Å3/Da / Density % sol: 62.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.60M Na/K2PO4, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97649 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97649 Å / Relative weight: 1
ReflectionResolution: 2.6→37.42 Å / Num. all: 67606 / Num. obs: 67606 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 9.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.698 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1REQ

1req


Resolution: 2.6→37.42 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.91 / SU B: 20.894 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.385 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24341 1152 1.7 %RANDOM
Rwork0.21712 ---
all0.21758 66447 --
obs0.21758 66447 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å22.7 Å2
2---1.18 Å20 Å2
3---1.8 Å2
Refinement stepCycle: LAST / Resolution: 2.6→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10642 0 4 84 10730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210876
X-RAY DIFFRACTIONr_bond_other_d0.0020.027153
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.9614786
X-RAY DIFFRACTIONr_angle_other_deg0.949317488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46151430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5124.283446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96151711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4011562
X-RAY DIFFRACTIONr_chiral_restr0.0610.21692
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022144
X-RAY DIFFRACTIONr_nbd_refined0.2070.22383
X-RAY DIFFRACTIONr_nbd_other0.1780.27230
X-RAY DIFFRACTIONr_nbtor_refined0.1760.25440
X-RAY DIFFRACTIONr_nbtor_other0.0840.25610
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2227
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0180.21
X-RAY DIFFRACTIONr_mcbond_it0.4151.57282
X-RAY DIFFRACTIONr_mcbond_other0.0591.52906
X-RAY DIFFRACTIONr_mcangle_it0.701211337
X-RAY DIFFRACTIONr_scbond_it0.94734036
X-RAY DIFFRACTIONr_scangle_it1.5564.53446
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3949tight positional0.030.05
11A4260medium positional0.030.5
22B312loose positional0.575
11A3949tight thermal1.110
11A4260medium thermal1.1810
22B312loose thermal1.6210
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 53 -
Rwork0.343 4664 -
obs--94.6 %
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)
12.0538-0.0646-0.5320.5480.12850.6306-0.14070.3324-0.2991-0.0240.0333-0.19940.12470.11310.1074-0.0564-0.0353-0.0009-0.023-0.041-0.048-27.2312.9499-32.3537
21.05570.1099-0.14540.8789-0.00330.71810.02550.14120.19110.1003-0.02620.2765-0.1916-0.12760.0008-0.0327-0.03650.0174-0.1056-0.0089-0.073-64.881829.2415-20.18
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA27 - 74517 - 735
2X-RAY DIFFRACTION2BB38 - 75728 - 747

+
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