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- PDB-5c4n: CobK precorrin-6A reductase -

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Basic information

Entry
Database: PDB / ID: 5c4n
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Precorrin-6A reductase
Function and homology information
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.63 Å
AuthorsGu, S. / Pickersgill, R.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I013334/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of CobK
Authors: Gu, S.
History
DepositionJun 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: 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 6, 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
D: Precorrin-6A reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8202
Polymers26,0771
Non-polymers7431
Water4,684260
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-3 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.870, 73.140, 103.220
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: 26076.875 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 (bacteria) / References: UniProt: O68098, precorrin-6A reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.63→42.17 Å / Num. obs: 32962 / % possible obs: 100 % / Redundancy: 7.4 % / Net I/σ(I): 19.4
Reflection shellResolution: 1.63→1.72 Å / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 1.63→42.17 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.741 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 1645 5 %RANDOM
Rwork0.17465 ---
obs0.17632 31240 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.703 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.63→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 48 260 2096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191881
X-RAY DIFFRACTIONr_bond_other_d0.0020.021800
X-RAY DIFFRACTIONr_angle_refined_deg2.3031.9932580
X-RAY DIFFRACTIONr_angle_other_deg0.99434118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3755242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44122.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84615259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4991516
X-RAY DIFFRACTIONr_chiral_restr0.1340.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212127
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02426
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_it2.461.902974
X-RAY DIFFRACTIONr_mcbond_other2.4511.896973
X-RAY DIFFRACTIONr_mcangle_it3.7512.8381214
X-RAY DIFFRACTIONr_mcangle_other3.7572.8431215
X-RAY DIFFRACTIONr_scbond_it3.692.358907
X-RAY DIFFRACTIONr_scbond_other3.6912.362908
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4993.3741367
X-RAY DIFFRACTIONr_long_range_B_refined9.24918.0552295
X-RAY DIFFRACTIONr_long_range_B_other8.97917.1752179
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 119 -
Rwork0.244 2275 -
obs--100 %

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