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- PDB-4e16: Precorrin-4 C(11)-methyltransferase from Clostridium difficile -

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Basic information

Entry
Database: PDB / ID: 4.0E+16
TitlePrecorrin-4 C(11)-methyltransferase from Clostridium difficile
Componentsprecorrin-4 C(11)-methyltransferase
KeywordsTRANSFERASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


precorrin-4 C11-methyltransferase activity / : / cobalamin biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / methylation
Similarity search - Function
Cobalamin (vitamin B12) biosynthesis CobM/CbiF, precorrin-4 C11-methyltransferase / Uroporphyrin-III C-methyltransferase signature 1. / Uroporphiryn-III C-methyltransferase, conserved site / Tetrapyrrole methylase, N-terminal domain / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases ...Cobalamin (vitamin B12) biosynthesis CobM/CbiF, precorrin-4 C11-methyltransferase / Uroporphyrin-III C-methyltransferase signature 1. / Uroporphiryn-III C-methyltransferase, conserved site / Tetrapyrrole methylase, N-terminal domain / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cobalt-precorrin-4 C(11)-methyltransferase (Cobalt-precorrin-3 methylase)
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsOsipiuk, J. / Nocek, B. / Makowska-Grzyska, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Precorrin-4 C(11)-methyltransferase from Clostridium difficile
Authors: Osipiuk, J. / Nocek, B. / Makowska-Grzyska, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: precorrin-4 C(11)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)28,2211
Polymers28,2211
Non-polymers00
Water0
1
A: precorrin-4 C(11)-methyltransferase

A: precorrin-4 C(11)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)56,4422
Polymers56,4422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4330 Å2
ΔGint-18 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.245, 60.245, 147.955
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein precorrin-4 C(11)-methyltransferase / precorrin-3 methylase


Mass: 28221.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: cbiF, CD630_34260 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q180S3, Transferases; Transferring one-carbon groups; Methyltransferases

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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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 20% PEG3350, 0.2 M sodium thiocyanate, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.49→55.797 Å / Num. all: 10113 / Num. obs: 10113 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 82 Å2 / Rmerge(I) obs: 0.098 / Χ2: 1.489 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.49-2.538.90.9242.594770.96497.1
2.53-2.5810.20.9614890.894100
2.58-2.6311.10.9644890.963100
2.63-2.68120.7834960.941100
2.68-2.7412.50.745041.051100
2.74-2.812.90.5914791.084100
2.8-2.8712.90.5254971.09100
2.87-2.9513.10.3854921.168100
2.95-3.04130.3355091.174100
3.04-3.14130.2274991.285100
3.14-3.2512.90.2114901.331100
3.25-3.3812.80.1685041.456100
3.38-3.5312.80.1335171.625100
3.53-3.7212.80.114981.715100
3.72-3.9512.70.1015141.816100
3.95-4.2612.50.0885222.047100
4.26-4.6912.30.0825132.003100
4.69-5.3611.90.0755282.071100
5.36-6.7511.30.0755432.25399.8
6.75-509.70.0715532.64791.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NDC

3ndc


Resolution: 2.49→41 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 1 / SU B: 29.949 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.439 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 495 4.9 %RANDOM
Rwork0.2043 ---
all0.2069 10064 --
obs0.2069 10064 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.22 Å2 / Biso mean: 98.824 Å2 / Biso min: 22.26 Å2
Baniso -1Baniso -2Baniso -3
1-3.53 Å20 Å20 Å2
2--3.53 Å20 Å2
3----7.06 Å2
Refinement stepCycle: LAST / Resolution: 2.49→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 0 0 1773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021799
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.9772432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3065227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.53726.08174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.45715336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.485155
X-RAY DIFFRACTIONr_chiral_restr0.1210.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211306
LS refinement shellResolution: 2.49→2.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.522 37 -
Rwork0.417 545 -
all-582 -
obs-582 92.82 %
Refinement TLS params.Method: refined / Origin x: 21.5528 Å / Origin y: 15.7019 Å / Origin z: 8.724 Å
111213212223313233
T0.285 Å20.0561 Å2-0.0344 Å2-0.4526 Å20.1303 Å2--0.182 Å2
L2.902 °22.5366 °21.1964 °2-2.8836 °20.9896 °2--2.9465 °2
S0.0222 Å °-0.175 Å °-0.1817 Å °0.1878 Å °0.0543 Å °0.0134 Å °0.0966 Å °0.1445 Å °-0.0765 Å °

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