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- PDB-2yxd: Crystal Structure of Cobalamin biosynthesis precorrin 8W decarbox... -

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Basic information

Entry
Database: PDB / ID: 2yxd
TitleCrystal Structure of Cobalamin biosynthesis precorrin 8W decarboxylase (cbiT)
ComponentsProbable cobalt-precorrin-6Y C(15)-methyltransferase [decarboxylating]
KeywordsTRANSFERASE / Alpha and beta protein (a/b) Class / Methyltransferase superfamily / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


cobalt-precorrin-6B (C15)-methyltransferase [decarboxylating] / corrin biosynthetic process / protein methyltransferase activity / cobalamin biosynthetic process
Similarity search - Function
Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) CbiT / Cobalamin biosynthesis, precorrin-6Y methyltransferase, CbiT subunit / Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating)
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsPadmanabhan, B. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Cobalamin biosynthesis precorrin 8W decarboxylase (cbiT)
Authors: Padmanabhan, B. / Bessho, Y. / Yokoyama, S.
History
DepositionApr 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable cobalt-precorrin-6Y C(15)-methyltransferase [decarboxylating]
B: Probable cobalt-precorrin-6Y C(15)-methyltransferase [decarboxylating]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8295
Polymers41,4412
Non-polymers3873
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Probable cobalt-precorrin-6Y C(15)-methyltransferase [decarboxylating]
B: Probable cobalt-precorrin-6Y C(15)-methyltransferase [decarboxylating]
hetero molecules

A: Probable cobalt-precorrin-6Y C(15)-methyltransferase [decarboxylating]
B: Probable cobalt-precorrin-6Y C(15)-methyltransferase [decarboxylating]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,65710
Polymers82,8834
Non-polymers7756
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area9930 Å2
ΔGint-108 kcal/mol
Surface area28040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.442, 93.442, 81.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Probable cobalt-precorrin-6Y C(15)-methyltransferase [decarboxylating] / Cobalamin Biosynthesis Precorrin 8W Decarboxylases


Mass: 20720.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: cbiT / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL-X
References: UniProt: Q57836, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 298 K / Method: oil batch / pH: 6
Details: 50% PEG 400, 0.1M MES, pH 6.0, OIL BATCH, temperature 298.0K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97891, 0.90000, 0.97928
DetectorType: RIGAKU JUPITER 210 / Detector: CCD
RadiationMonochromator: Si double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978911
20.91
30.979281
ReflectionResolution: 2.3→50 Å / Num. all: 16507 / Num. obs: 16322 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Rmerge(I) obs: 0.089
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.36 / Num. unique all: 1539 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.744 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.453 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27322 788 5.1 %RANDOM
Rwork0.19793 ---
obs0.20171 14721 94.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.032 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å20 Å2
2--1.8 Å20 Å2
3----3.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 22 108 2893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0222815
X-RAY DIFFRACTIONr_angle_refined_deg2.4861.9743793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2525358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.4226115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.85815536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1031510
X-RAY DIFFRACTIONr_chiral_restr0.1950.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022026
X-RAY DIFFRACTIONr_nbd_refined0.270.21422
X-RAY DIFFRACTIONr_nbtor_refined0.3330.21970
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2147
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.320.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.29
X-RAY DIFFRACTIONr_mcbond_it1.5531.51842
X-RAY DIFFRACTIONr_mcangle_it2.45522886
X-RAY DIFFRACTIONr_scbond_it4.13931085
X-RAY DIFFRACTIONr_scangle_it6.3764.5907
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 57 -
Rwork0.205 896 -
obs--80.83 %

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