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- PDB-9frc: Architectural insights into spatially distinct corrin and metal b... -

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Basic information

Entry
Database: PDB / ID: 9frc
TitleArchitectural insights into spatially distinct corrin and metal binding sites of CobN
ComponentsCobn protein
KeywordsBIOSYNTHETIC PROTEIN / Cobaltochelatase/CobN/cobalamin biosynthesis
Function / homologycobaltochelatase / cobaltochelatase activity / Cobaltochelatase, CobN subunit / CobN/magnesium chelatase / CobN/Magnesium Chelatase / cobalamin biosynthetic process / : / Cobaltochelatase subunit CobN
Function and homology information
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsPickersgill, R.W. / Brown, D.G. / Ladakis, D. / Warren, M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/001946/1 United Kingdom
CitationJournal: To Be Published
Title: Architecture of CobN
Authors: Pickersgill, R.W. / Brown, D.G. / Ladakis, D. / Warren, M.J.
History
DepositionJun 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cobn protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9372
Polymers42,0581
Non-polymers8791
Water39622
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16700 Å2
Unit cell
Length a, b, c (Å)62.320, 73.600, 86.470
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 Cobn protein


Mass: 42057.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This is the C-terminal domain of CobN / Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: ATCC 23456 / Gene: BMEI0695 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) pLysS / References: UniProt: Q8YHV1
#2: Chemical ChemComp-A1IFT / Hydrogenobyrinic acid a,c-diamide / 3-[(1~{R},2~{S},3~{S},5~{Z},7~{S},8~{S},9~{Z},13~{S},14~{Z},17~{R},18~{R},19~{R})-2,7-bis(2-azanyl-2-oxidanylidene-ethyl)-18-(2-hydroxy-2-oxoethyl)-3,13,17-tris(3-hydroxy-3-oxopropyl)-1,2,5,7,12,12,15,17-octamethyl-3,8,13,18,19,22-hexahydrocorrin-8-yl]propanoic acid


Mass: 879.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H62N6O12 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Lithium sulfate, 30% PEG 4000, 0.1M Tris pH 8.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.58→56.05 Å / Num. obs: 13012 / % possible obs: 99.6 % / Redundancy: 18.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.6
Reflection shellResolution: 2.58→2.65 Å / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4484

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→56.05 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.605 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 2.311 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27526 630 4.9 %RANDOM
Rwork0.1836 ---
obs0.18789 12341 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.068 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.58→56.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 0 22 3052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123102
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162861
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.8314226
X-RAY DIFFRACTIONr_angle_other_deg0.6021.7626545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9565383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.5258.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27710467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02760
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_it6.1016.0531535
X-RAY DIFFRACTIONr_mcbond_other6.0996.0521535
X-RAY DIFFRACTIONr_mcangle_it8.39310.8881917
X-RAY DIFFRACTIONr_mcangle_other8.39210.8911918
X-RAY DIFFRACTIONr_scbond_it7.5956.8511567
X-RAY DIFFRACTIONr_scbond_other7.5886.851566
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.18612.2032310
X-RAY DIFFRACTIONr_long_range_B_refined13.2358.733342
X-RAY DIFFRACTIONr_long_range_B_other13.22858.733343
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.58→2.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 54 -
Rwork0.274 870 -
obs--98.19 %

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