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- PDB-4fdv: CobH from Rhodobacter capsulatus (SB1003) in complex with HBA -

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Basic information

Entry
Database: PDB / ID: 4fdv
TitleCobH from Rhodobacter capsulatus (SB1003) in complex with HBA
ComponentsPrecorrin-8X methylmutase
KeywordsISOMERASE / doubly wound sheet / sigmatrophic rearrangement / Hydrogenobyrinic acid
Function / homology
Function and homology information


precorrin-8X methylmutase / precorrin-8X methylmutase activity / cobalamin biosynthetic process
Similarity search - Function
Cobalamin biosynthesis CobH/CbiC, precorrin-8X methylmutase / Cobalamin biosynthesis precorrin-8X methylmutase CobH/CbiC / Precorrin-8X methylmutase CobH/CbiC superfamily / Precorrin-8X methylmutase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-0UK / Precorrin-8X methylmutase
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsPickersgill, R.W. / Schroeder, S. / Deery, E. / Warren, M.J.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis.
Authors: Deery, E. / Schroeder, S. / Lawrence, A.D. / Taylor, S.L. / Seyedarabi, A. / Waterman, J. / Wilson, K.S. / Brown, D. / Geeves, M.A. / Howard, M.J. / Pickersgill, R.W. / Warren, M.J.
History
DepositionMay 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Precorrin-8X methylmutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0844
Polymers22,0171
Non-polymers1,0673
Water4,035224
1
A: Precorrin-8X methylmutase
hetero molecules

A: Precorrin-8X methylmutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1688
Polymers44,0332
Non-polymers2,1346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5970 Å2
ΔGint-23 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.251, 66.028, 48.480
Angle α, β, γ (deg.)90.00, 98.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Precorrin-8X methylmutase


Mass: 22016.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Strain: ATCC BAA-309 / NBRC 16581 / SB1003 / Gene: cobH, RCAP_rcc02046 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / References: UniProt: D5AV08, precorrin-8X methylmutase
#2: Chemical ChemComp-0UK / 3-[(1R,2R,3R,5R,6S,7R,9Z,12S,13S,14Z,17S,18S,19R)-2,13,18-tris(2-hydroxy-2-oxoethyl)-3,12,17-tris(3-hydroxy-3-oxopropyl)-3,5,8,8,13,15,18,19-octamethyl-1,2,5,6,7,12,17,22-octahydrocorrin-7-yl]propanoic acid


Mass: 882.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H62N4O14
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 8000, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2010 / Details: Silicon 111
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.68→34.7 Å / Num. all: 24994 / Num. obs: 24344 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 16.9
Reflection shellResolution: 1.68→1.77 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 6.6 / Rsym value: 0.174 / % possible all: 95.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I1H

1i1h


Resolution: 1.68→33.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.671 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20037 1244 5.1 %RANDOM
Rwork0.16535 ---
obs0.16713 23090 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.423 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.68→33.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 75 224 1830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221649
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.742.0242259
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9415211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30523.16760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01715249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7411514
X-RAY DIFFRACTIONr_chiral_restr0.1010.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211240
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5881.51045
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08521670
X-RAY DIFFRACTIONr_scbond_it1.9933604
X-RAY DIFFRACTIONr_scangle_it3.3234.5587
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.722 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 84 -
Rwork0.246 1653 -
obs--94.25 %

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