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- PDB-3hjg: Crystal structure of putative alpha-ribazole-5'-phosphate phospha... -

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Basic information

Entry
Database: PDB / ID: 3hjg
TitleCrystal structure of putative alpha-ribazole-5'-phosphate phosphatase CobC FROM Vibrio parahaemolyticus
ComponentsPutative alpha-ribazole-5'-phosphate phosphatase CobC
KeywordsHYDROLASE / PHOSPHATASE / PSI-2 / NYSGXRC / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


alpha-ribazole phosphatase activity / cobalamin biosynthetic process
Similarity search - Function
Alpha-ribazole phosphatase, CobC / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative alpha-ribazole-5'-phosphate phosphatase CobC
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsPatskovsky, Y. / Toro, R. / Morano, C. / Rutter, M. / Iizuka, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative alpha-ribazole-5' -phosphate phosphatase FROM Vibrio parahaemolyticus
Authors: Patskovsky, Y. / Toro, R. / Morano, C. / Rutter, M. / Iizuka, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMay 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative alpha-ribazole-5'-phosphate phosphatase CobC
B: Putative alpha-ribazole-5'-phosphate phosphatase CobC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3436
Polymers47,9582
Non-polymers3844
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-80 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.215, 107.215, 206.717
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
/ NCS ensembles :
ID
1
2
3

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Components

#1: Protein Putative alpha-ribazole-5'-phosphate phosphatase CobC


Mass: 23979.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VP1307 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-CODON+RIL(STRATAGENE) / References: UniProt: Q87Q43
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 6.2 Å3/Da / Density % sol: 80.17 %
Description: DIFFRACTION DATA WERE CORRECTED AND TRUNCATED DUE TO ANISOTROPY
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5% ISOPROPANOL, 2000 MM AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 7.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 37362 / % possible obs: 99.9 % / Observed criterion σ(I): -0.5 / Redundancy: 6.5 % / Rsym value: 0.132 / Net I/σ(I): 5
Reflection shellResolution: 2.61→2.7 Å / Redundancy: 5 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 0.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
SHELXDphasing
REFMAC5.3.0034refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.934 / SU B: 20.729 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R: 0.371 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28009 849 3.1 %RANDOM
Rwork0.26275 ---
obs0.26331 26642 90.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 127.928 Å2
Baniso -1Baniso -2Baniso -3
1--4.25 Å20 Å20 Å2
2---4.25 Å20 Å2
3---8.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3194 0 20 0 3214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213285
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.944477
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.925404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2624.834151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.32115551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.031515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022465
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1290.31463
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.52169
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.5155
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0780.355
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.52
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.89522063
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.50433260
X-RAY DIFFRACTIONr_scbond_it3.93241394
X-RAY DIFFRACTIONr_scangle_it6.26261216
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1102tight positional0.720.1
2436tight positional0.460.1
3676tight positional0.560.1
1102tight thermal2.425
2436tight thermal4.915
3676tight thermal3.825
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.496 8 -
Rwork0.598 385 -
obs--18.29 %

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