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- PDB-4x7g: CobK precorrin-6A reductase -

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Basic information

Entry
Database: PDB / ID: 4x7g
TitleCobK precorrin-6A reductase
ComponentsPrecorrin-6A reductase
KeywordsOXIDOREDUCTASE / NADP binding
Function / homologyprecorrin-6A reductase / precorrin-6A reductase activity / Precorrin-6x reductase / Precorrin-6x reductase CbiJ/CobK / Precorrin-6x reductase domain profile. / cobalamin biosynthetic process / Chem-3Y8 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Precorrin-6A reductase
Function and homology information
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.22 Å
AuthorsGu, S. / Deery, E. / Warren, M.J. / 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
DepositionDec 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8743
Polymers26,2181
Non-polymers1,6562
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-5 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.090, 60.280, 76.250
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: 26217.561 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
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (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: Chemical ChemComp-3Y8 / 3-[(1R,2S,3S,7S,11S,16S,17R,18R,19R)-2,7,12,18-tetrakis(2-hydroxy-2-oxoethyl)-3,13-bis(3-hydroxy-3-oxopropyl)-1,2,5,7,11,17-hexamethyl-17-(3-oxidanyl-3-oxidanylidene-prop-1-enyl)-3,6,8,10,15,16,18,19,21,24-decahydrocorrin-8-yl]propanoic acid


Mass: 912.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H60N4O16
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8 / Details: 18% w/v PEG 3350, 0.2 M NH4 Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.22→47.3 Å / Num. obs: 73880 / % possible obs: 99.2 % / Redundancy: 7.09 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 16.254
Reflection shellResolution: 1→1.22 Å / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 6.6 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Aimlessdata scaling
XSCALEdata scaling
SHELXphasing
XSCALEdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.22→47.29 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.719 / SU ML: 0.032 / Cross valid method: FREE R-VALUE / ESU R: 0.041 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19702 3676 5 %RANDOM
Rwork0.1771 ---
obs0.17809 69845 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.163 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.22→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 113 186 2135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192043
X-RAY DIFFRACTIONr_bond_other_d0.0060.021948
X-RAY DIFFRACTIONr_angle_refined_deg2.8312.0252826
X-RAY DIFFRACTIONr_angle_other_deg1.4513.014467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6155262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05222.26775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98215268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5411518
X-RAY DIFFRACTIONr_chiral_restr0.3110.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0212311
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02452
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_it1.4871.4171018
X-RAY DIFFRACTIONr_mcbond_other1.4421.4161017
X-RAY DIFFRACTIONr_mcangle_it2.0612.1321275
X-RAY DIFFRACTIONr_mcangle_other2.0612.1331276
X-RAY DIFFRACTIONr_scbond_it3.191.6571025
X-RAY DIFFRACTIONr_scbond_other3.1921.6571023
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9552.3991546
X-RAY DIFFRACTIONr_long_range_B_refined5.53212.8142416
X-RAY DIFFRACTIONr_long_range_B_other5.53112.8152417
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.215→1.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 269 -
Rwork0.289 5115 -
obs--99.04 %

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