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- PDB-5c4r: CobK precorrin-6A reductase -

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Basic information

Entry
Database: PDB / ID: 5c4r
TitleCobK precorrin-6A reductase
ComponentsPrecorrin-6A reductase
KeywordsOXIDOREDUCTASE / CobK precorrin-6A reductase / NADP / Rossmann fold / Precorrin
Function / homologyprecorrin-6A reductase / precorrin-6A reductase activity / Precorrin-6x reductase / Precorrin-6x reductase CbiJ/CobK / Precorrin-6x reductase domain profile. / cobalamin biosynthetic process / Precorrin-6A reductase
Function and homology information
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.17 Å
AuthorsGu, S. / Pickersgill, R.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I013334/1 United Kingdom
CitationJournal: Sci Rep / Year: 2015
Title: Crystal structure of CobK reveals strand-swapping between Rossmann-fold domains and molecular basis of the reduced precorrin product trap.
Authors: Gu, S. / Sushko, O. / Deery, E. / Warren, M.J. / Pickersgill, R.W.
History
DepositionJun 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Precorrin-6A reductase


Theoretical massNumber of molelcules
Total (without water)26,0921
Polymers26,0921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.900, 75.300, 115.100
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 Precorrin-6A reductase / Precorrin-6X reductase


Mass: 26091.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria)
Gene: cobK, RCAP_rcc02043 / Plasmid: pET14B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O68098, precorrin-6A reductase
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: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8 / Details: 18% PEG3350, 0.2M NH4Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.13956 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13956 Å / Relative weight: 1
ReflectionResolution: 3.17→63.01 Å / Num. obs: 16610 / % possible obs: 98.16 % / Redundancy: 1.8 % / Net I/σ(I): 5.5
Reflection shellResolution: 3.17→3.34 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.6 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Aimlessdata scaling
SHELXphasing
SCALAdata scaling
RefinementResolution: 3.17→63.01 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.896 / SU B: 19.186 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23595 262 5 %RANDOM
Rwork0.17903 ---
obs0.18194 4968 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.305 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å2-0 Å20 Å2
2---0.05 Å20 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 3.17→63.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 0 0 1796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191838
X-RAY DIFFRACTIONr_bond_other_d0.0010.021782
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9592512
X-RAY DIFFRACTIONr_angle_other_deg0.81434075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6655243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45922.572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.28915260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3681516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212117
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
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_it2.8994.953978
X-RAY DIFFRACTIONr_mcbond_other2.8854.952977
X-RAY DIFFRACTIONr_mcangle_it4.8067.4161219
X-RAY DIFFRACTIONr_mcangle_other4.8057.4171220
X-RAY DIFFRACTIONr_scbond_it3.2645.352860
X-RAY DIFFRACTIONr_scbond_other3.2625.352861
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3347.8641294
X-RAY DIFFRACTIONr_long_range_B_refined7.73239.8271990
X-RAY DIFFRACTIONr_long_range_B_other7.73239.8411991
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.17→3.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 19 -
Rwork0.231 354 -
obs--98.16 %

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