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- PDB-2yxb: Crystal structure of the methylmalonyl-CoA mutase alpha-subunit f... -

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Basic information

Entry
Database: PDB / ID: 2yxb
TitleCrystal structure of the methylmalonyl-CoA mutase alpha-subunit from Aeropyrum pernix
ComponentsCoenzyme B12-dependent mutase
KeywordsISOMERASE / alpha/beta / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


cobalamin binding / isomerase activity / metal ion binding
Similarity search - Function
Methylmalonyl-CoA mutase, C-terminal / Cobalamin-binding domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Coenzyme B12-dependent mutase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsHanda, N. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the methylmalonyl-CoA mutase alpha-subunit from Aeropyrum pernix
Authors: Handa, N. / Bessho, Y. / Yokoyama, S.
History
DepositionApr 25, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coenzyme B12-dependent mutase


Theoretical massNumber of molelcules
Total (without water)17,9831
Polymers17,9831
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.902, 51.134, 54.564
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coenzyme B12-dependent mutase / Methylmalonyl-CoA mutase


Mass: 17982.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL-X / References: UniProt: Q9YBB1, methylmalonyl-CoA mutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.662207 Å3/Da / Density % sol: 26.00201 %
Crystal growTemperature: 293 K / Method: oil batch
Details: 0.4M Ammonium dihydrogen phosphate, oil batch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97884, 0.90000, 0.97938
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 15, 2006 / Details: mirrors
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978841
20.91
30.979381
ReflectionResolution: 1.8→50 Å / Num. obs: 11582 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rsym value: 0.067 / Net I/σ(I): 17.8
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.35 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→37.27 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.421 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24713 552 4.8 %RANDOM
Rwork0.21194 ---
obs0.21373 10970 99.56 %-
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: 33.745 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2--0.52 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 0 79 1153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0221087
X-RAY DIFFRACTIONr_bond_other_d0.0020.021089
X-RAY DIFFRACTIONr_angle_refined_deg2.16621461
X-RAY DIFFRACTIONr_angle_other_deg1.00232512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3655138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1480.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021194
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02212
X-RAY DIFFRACTIONr_nbd_refined0.2220.2231
X-RAY DIFFRACTIONr_nbd_other0.2550.21257
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.2753
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6331.5688
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.88821102
X-RAY DIFFRACTIONr_scbond_it4.4193399
X-RAY DIFFRACTIONr_scangle_it6.8354.5359
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.269 36
Rwork0.237 785

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