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- PDB-1f38: X-RAY CRYSTALLOGRAPHIC STRUCTURE OF PRECORRIN 8W DECARBOXYLASE, T... -

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Basic information

Entry
Database: PDB / ID: 1f38
TitleX-RAY CRYSTALLOGRAPHIC STRUCTURE OF PRECORRIN 8W DECARBOXYLASE, THE PRODUCT OF GENE MT0146 IN THE METHANOBACTERIUM THERMOAUTOTROPHICUM GENOME
ComponentsPRECORRIN-8W DECARBOXYLASE
KeywordsLYASE / Decarboxylase / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


cobalt-precorrin-6B (C15)-methyltransferase [decarboxylating] / cobalt-precorrin-6B C5-methyltransferase activity / anaerobic cobalamin biosynthetic process / protein methyltransferase activity / methylation
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 speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsKeller, J.P. / Smith, P.M. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Structure / Year: 2002
Title: The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase
Authors: Keller, J.P. / Smith, P.M. / Benach, J. / Christendat, D. / deTitta, G.T. / Hunt, J.F.
History
DepositionMay 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRECORRIN-8W DECARBOXYLASE
B: PRECORRIN-8W DECARBOXYLASE
C: PRECORRIN-8W DECARBOXYLASE
D: PRECORRIN-8W DECARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)84,4494
Polymers84,4494
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-70 kcal/mol
Surface area28990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.470, 194.760, 59.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a tetramer constructed from chains A -> D.

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Components

#1: Protein
PRECORRIN-8W DECARBOXYLASE


Mass: 21112.131 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Description: GENOMIC DNA / Gene: MT0146 / Plasmid: PET14A DERIVATIVE / Production host: Escherichia coli (E. coli) / References: UniProt: O26249
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop
Details: Magnesium Chloride, PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 26K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1.06884
DetectorType: MARRESEARCH / Detector: CCD / Date: May 19, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06884 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 54692 / Num. obs: 33548 / % possible obs: 73.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 13.2 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 25
Reflection shellResolution: 2.4→2.51 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.08 / % possible all: 91.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MAD / Resolution: 2.4→100 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: X-PLOR 3.851
RfactorNum. reflectionSelection details
Rfree0.291 31870 Random
Rwork0.236 --
all-54692 -
obs-33548 -
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 0 180 5748
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_d1.8

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