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- PDB-5n0g: Crystal Structure of CobH T85A (precorrin-8x methyl mutase) compl... -

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Basic information

Entry
Database: PDB / ID: 5n0g
TitleCrystal Structure of CobH T85A (precorrin-8x methyl mutase) complexed with C5 allyl-HBA
ComponentsPrecorrin-8X methylmutase
KeywordsISOMERASE / Complex
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-8F5 / Precorrin-8X methylmutase
Similarity search - Component
Biological speciesRhodobacter capsulatus SB 1003 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.57 Å
AuthorsNemoto-Smith, E.H. / Lawrence, A.D. / Brown, D.G. / Warren, M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K009249/1 United Kingdom
CitationJournal: To Be Published
Title: Novel cobalamin analogues and their application in the trafficking of cobalamin in bacteria, worms and plants
Authors: Lawrence, A.D. / Nemoto-Smith, E.H. / Deery, E.C. / Brown, D.G. / Tullet, J. / Brown, I.R. / Howard, M. / Boshoff, H.I. / Barry III, C.E. / Warren, M.J.
History
DepositionFeb 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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-8X methylmutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8553
Polymers21,8551
Non-polymers9992
Water3,315184
1
A: Precorrin-8X methylmutase
hetero molecules

A: Precorrin-8X methylmutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7096
Polymers43,7112
Non-polymers1,9984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5400 Å2
ΔGint-23 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.230, 66.630, 48.920
Angle α, β, γ (deg.)90.000, 99.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Precorrin-8X methylmutase


Mass: 21855.420 Da / Num. of mol.: 1 / Mutation: T85A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus SB 1003 (bacteria)
Gene: cobH, RCAP_rcc02046 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: D5AV08, precorrin-8X methylmutase
#2: Chemical ChemComp-8F5 / 3-[(1~{R},2~{S},3~{S},4~{Z},7~{S},8~{S},9~{Z},15~{R},17~{R},18~{R},19~{R})-2,7,18-tris(2-hydroxy-2-oxoethyl)-3,13,17-tris(3-hydroxy-3-oxopropyl)-1,2,7,12,12,15,17-heptamethyl-5-prop-2-enyl-3,8,15,18,19,21-hexahydrocorrin-8-yl]propanoic acid


Mass: 907.014 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H62N4O14
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 8000, 0.2M Calcium acetate hydrate, 0.1M Sodium cacodylate pH6.5, 20% methanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.57→48.38 Å / Num. obs: 57377 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 1.815 % / Biso Wilson estimate: 24.882 Å2 / CC1/2: 0.84 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.279 / Χ2: 0.694 / Net I/σ(I): 2.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.57-1.611.7930.7470.9941860.3781.02290.9
1.61-1.651.8030.611.1940760.4570.83490.1
1.65-1.71.8180.5061.3839010.5510.69290
1.7-1.761.8390.441.6438440.5840.60390.6
1.76-1.811.8650.362.0437880.6170.49791.9
1.81-1.881.8570.3322.1736480.6470.45991.9
1.88-1.951.8270.272.5534980.680.37493
1.95-2.031.7580.2432.7134560.7440.33892.9
2.03-2.121.8160.1963.0132720.8030.27292.7
2.12-2.221.7910.1783.2431470.8080.24892.3
2.22-2.341.8680.1663.4729980.8260.23194.8
2.34-2.481.8570.1633.6228680.8250.22793.9
2.48-2.651.8150.1673.6626680.7870.23394.3
2.65-2.871.720.1673.7124870.7680.23293
2.87-3.141.80.1723.922490.7710.24193.6
3.14-3.511.7890.1853.9820890.7820.25993.5
3.51-4.051.8530.1874.1418530.7340.26294.6
4.05-4.961.7760.1874.1115230.7480.26293
4.96-7.021.7280.2064.0112000.7730.28895
7.02-48.381.9010.2054.276260.8010.28989.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
xia20.3.8.0data reduction
REFMACphasing
RefinementResolution: 1.57→48.38 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.053 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.094
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 1461 4.7 %RANDOM
Rwork0.1723 ---
obs0.1753 29762 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 71.85 Å2 / Biso mean: 23.096 Å2 / Biso min: 10.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0 Å20.67 Å2
2--0.04 Å2-0 Å2
3----0.54 Å2
Refinement stepCycle: final / Resolution: 1.57→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1530 0 71 184 1785
Biso mean--20.35 31.78 -
Num. residues----208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0191670
X-RAY DIFFRACTIONr_bond_other_d0.0020.021649
X-RAY DIFFRACTIONr_angle_refined_deg2.7312.0212292
X-RAY DIFFRACTIONr_angle_other_deg1.27833780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6675215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2322.95161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58415251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7211515
X-RAY DIFFRACTIONr_chiral_restr0.1720.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211908
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02351
X-RAY DIFFRACTIONr_rigid_bond_restr5.64733317
X-RAY DIFFRACTIONr_sphericity_free21.5445132
X-RAY DIFFRACTIONr_sphericity_bonded6.22653337
LS refinement shellResolution: 1.57→1.611 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 111 -
Rwork0.277 2209 -
all-2320 -
obs--99.74 %
Refinement TLS params.Method: refined / Origin x: -14.85 Å / Origin y: 33.609 Å / Origin z: 20.827 Å
111213212223313233
T0.0129 Å20.0008 Å2-0.0005 Å2-0.018 Å20.0078 Å2--0.0188 Å2
L0.676 °2-0.1219 °2-0.2352 °2-0.6277 °20.1675 °2--0.7918 °2
S-0.0234 Å °0.0381 Å °0.0362 Å °-0.0559 Å °0.0371 Å °0.0192 Å °-0.0602 Å °-0.0356 Å °-0.0137 Å °

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