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- PDB-2w6k: The crystal structure at 1.7 A resolution of CobE, a protein from... -

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Basic information

Entry
Database: PDB / ID: 2w6k
TitleThe crystal structure at 1.7 A resolution of CobE, a protein from the cobalamin (vitamin B12) biosynthetic pathway
ComponentsCOBE
KeywordsBIOSYNTHETIC PROTEIN / COBALAMIN / COBE / PSEUDOMONAS AERUGINOSA / VITAMIN B12
Function / homology
Function and homology information


cobalamin biosynthetic process
Similarity search - Function
CobE/GbiG C-terminal domain / CobE/GbiG C-terminal domain / CobE/GbiG C-terminal domain superfamily / : / Cobalamin synthesis G C-terminus / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CobE/GbiG C-terminal domain-containing protein
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsVevodova, J. / Smith, D. / McGoldrick, H. / Deery, E. / Murzin, A.G. / Warren, M.J. / Wilson, K.S.
Citation
Journal: To be Published
Title: The Crystal Structure at 1.7 A Resolution of Cobe, a Protein from the Cobalamin (Vitamin B12) Biosynthetic Pathway
Authors: Vevodova, J. / Smith, D. / Mcgoldrick, H. / Deery, E. / Murzin, A.G. / Warren, M.J. / Wilson, K.S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization and Preliminary Structure Analysis of Cobe, an Essential Protein of Cobalamin (Vitamin B12) Biosynthesis.
Authors: Vevodova, J. / Graham, R.M. / Raux, E. / Warren, M.J. / Wilson, K.S.
History
DepositionDec 18, 2008Deposition site: PDBE / Processing site: PDBE
SupersessionDec 30, 2008ID: 2BSN
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
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_conn.pdbx_leaving_atom_flag
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COBE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9046
Polymers15,4361
Non-polymers4685
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.729, 41.271, 87.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein COBE


Mass: 15435.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HZQ0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35 % / Description: NONE
Crystal growDetails: 0.1M MES PH6.9, 2M AMMONIUM SULPHATE, 5% DIOXANE

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONESRF ID14-110.934
SYNCHROTRONESRF BM1420.95372, 0.97925, 0.97944
Detector
TypeIDDetector
MARRESEARCH1IMAGE PLATE
ADSC CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
20.953721
30.979251
40.979441
ReflectionResolution: 1.7→45 Å / Num. obs: 13347 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 12.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 7.1 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.7→30.1 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.349 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MAD DATASETS TO 2.5A RESOLUTION WERE USED TO OBTAIN THE INITIAL MODEL. SAD DATA TO 1.7A RESOLUTION WERE USED TO EXTEND THE RESOLUTION PRIOR THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 619 4.8 %RANDOM
Rwork0.199 ---
obs0.202 12361 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2--0.69 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 28 97 1178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211106
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.692.0311490
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0995145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25320.46543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15915188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8991517
X-RAY DIFFRACTIONr_chiral_restr0.1160.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02810
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.2538
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2734
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0561.5723
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81421120
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3933401
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7974.5368
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.246 37
Rwork0.244 852

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