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- PDB-2w6l: The crystal structure at 1.7 A resolution of CobE, a protein from... -

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Basic information

Entry
Database: PDB / ID: 2w6l
TitleThe crystal structure at 1.7 A resolution of CobE, a protein from the cobalamin (vitamin B12) biosynthetic pathway
ComponentsCOBE
KeywordsBIOSYNTHETIC PROTEIN / PSEUDOMONAS AERUGINOSA / COBE / COBALAMIN / PRECORRIN / NOVEL FOLD / 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: 1.89 Å
AuthorsVevodova, J. / Smith, D. / McGoldrick, H. / Deery, E. / Murzin, A.G. / Warren, M.J. / Wilson, K.S.
CitationJournal: 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.
History
DepositionDec 18, 2008Deposition site: PDBE / Processing site: PDBE
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 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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

Downloads & links

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Assembly

Deposited unit
A: COBE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4675
Polymers15,0901
Non-polymers3764
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.862, 41.070, 87.411
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: 15090.366 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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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: 0.1 MES PH 6.9, 2M AMMONIUM SULPHATE, 5% DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 9752 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.8
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 6.4 / % possible all: 73

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Processing

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

Resolution: 1.89→43.69 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.742 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 462 4.8 %RANDOM
Rwork0.212 ---
obs0.215 9083 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20 Å2
2--1.32 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.89→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1013 0 22 89 1124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211050
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8862.0371418
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0375136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.79920.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78115178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8211516
X-RAY DIFFRACTIONr_chiral_restr0.1190.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02767
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.2485
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2692
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4050.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.411.5704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.40621075
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8613374
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8154.5343
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: 1.89→1.94 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 28
Rwork0.209 580

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