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- PDB-4au1: Crystal Structure of CobH (precorrin-8x methyl mutase) complexed ... -

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Basic information

Entry
Database: PDB / ID: 4au1
TitleCrystal Structure of CobH (precorrin-8x methyl mutase) complexed with C5 desmethyl-HBA
ComponentsPRECORRIN-8X METHYLMUTASE
KeywordsISOMERASE / PRECORRIN / HBA
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
DESMETHYL-HBA / Precorrin-8X methylmutase
Similarity search - Component
Biological speciesRHODOBACTER CAPSULATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsDeery, E. / Lawrence, A.D. / Schroeder, S. / Taylor, S.L. / Seyedarabi, A. / Vevodova, J. / Wilson, K.S. / Brown, D. / Geeves, M.A. / Howard, M.J. ...Deery, E. / Lawrence, A.D. / Schroeder, S. / Taylor, S.L. / Seyedarabi, A. / Vevodova, J. / Wilson, K.S. / Brown, D. / Geeves, M.A. / Howard, M.J. / Pickersgill, R.W. / Warren, M.J.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: An Enzyme-Trap Approach Allows Isolation of Intermediates in Cobalamin Biosynthesis
Authors: Deery, E. / Schroeder, S. / Lawrence, A.D. / Taylor, S.L. / Seyedarabi, A. / Waterman, J. / Wilson, K.S. / Brown, D. / Geeves, M.A. / Howard, M.J. / Pickersgill, R.W. / Warren, M.J.
History
DepositionMay 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Oct 17, 2012Group: Data collection / Database references
Revision 1.3Nov 14, 2012Group: Database references
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)25,1513
Polymers24,1881
Non-polymers9632
Water5,026279
1
A: PRECORRIN-8X METHYLMUTASE
hetero molecules

A: PRECORRIN-8X METHYLMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3026
Polymers48,3762
Non-polymers1,9264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7620 Å2
ΔGint-68.6 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.550, 65.710, 48.050
Angle α, β, γ (deg.)90.00, 99.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PRECORRIN-8X METHYLMUTASE


Mass: 24188.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Strain: SB1003 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: D5AV08, precorrin-8X methylmutase
#2: Chemical ChemComp-P8X / DESMETHYL-HBA


Mass: 866.950 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H58N4O14
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsC5 DES METHYL HBA (P8X): ALSO C15 APPEARS TO BE SP3 CF PREVIOUSLY DEPOSITED STRUCTURES
Sequence detailsGENBANK ENTRY RCAP_RCC02046

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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: 2.27 Å3/Da / Density % sol: 45.86 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.45→47.79 Å / Num. obs: 37503 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 19.09 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 20.2
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.2 / % possible all: 98.3

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→47.79 Å / Cor.coef. Fo:Fc: 0.9672 / Cor.coef. Fo:Fc free: 0.9628 / SU R Cruickshank DPI: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.062 / SU Rfree Blow DPI: 0.061 / SU Rfree Cruickshank DPI: 0.058
RfactorNum. reflection% reflectionSelection details
Rfree0.178 1873 4.99 %RANDOM
Rwork0.1605 ---
obs0.1613 37503 97.67 %-
Displacement parametersBiso mean: 21.13 Å2
Baniso -1Baniso -2Baniso -3
1-1.5577 Å20 Å2-1.1397 Å2
2---1.0615 Å20 Å2
3----0.4961 Å2
Refine analyzeLuzzati coordinate error obs: 0.154 Å
Refinement stepCycle: LAST / Resolution: 1.45→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 67 279 1878
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011723HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.082412HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d603SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes34HARMONIC2
X-RAY DIFFRACTIONt_gen_planes275HARMONIC5
X-RAY DIFFRACTIONt_it1723HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.16
X-RAY DIFFRACTIONt_other_torsion13.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion226SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2417SEMIHARMONIC4
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2031 146 5.01 %
Rwork0.2001 2767 -
all0.2002 2913 -
obs--97.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5646-0.0429-0.06370.44630.17230.3648-0.02210.0309-0.012-0.04020.02760.0631-0.0354-0.0398-0.0055-0.02050.00470.0048-0.02750.0157-0.0164-14.66833.177820.615
20.28560.4062.07720.31510.43212.18030.0282-0.01550.1564-0.0573-0.0715-0.0377-0.0310.03240.0433-0.0132-0.0240.00590.00710.0003-0.00390.019234.283713.39
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 2-209
2X-RAY DIFFRACTION2CHAIN A AND RESID 1210

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