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- PDB-3ey8: Structure from the mobile metagenome of V. Pseudocholerae. VPC_CASS1 -

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Basic information

Entry
Database: PDB / ID: 3ey8
TitleStructure from the mobile metagenome of V. Pseudocholerae. VPC_CASS1
ComponentsBiphenyl-2,3-diol 1,2-dioxygenase III-related protein
KeywordsOXIDOREDUCTASE / Integron Cassette protein / Dioxygenase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Biphenyl-2,3-diol 1,2-dioxygenase III-related protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHarrop, S.J. / Deshpande, C.N. / Sureshan, V. / Boucher, Y. / Xu, X. / Cui, H. / Chang, C. / Edwards, A. / Joachimiak, A. / Savchenko, A. ...Harrop, S.J. / Deshpande, C.N. / Sureshan, V. / Boucher, Y. / Xu, X. / Cui, H. / Chang, C. / Edwards, A. / Joachimiak, A. / Savchenko, A. / Curmi, P.M.G. / Mabbutt, B.C. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure from the mobile metagenome of V. Pseudocholerae. VPC_CASS1
Authors: Harrop, S.J. / Deshpande, C.N. / Sureshan, V. / Boucher, Y. / Xu, X. / Cui, H. / Chang, C. / Edwards, A. / Joachimiak, A. / Savchenko, A. / Curmi, P.M.G. / Mabbutt, B.C.
History
DepositionOct 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Biphenyl-2,3-diol 1,2-dioxygenase III-related protein
B: Biphenyl-2,3-diol 1,2-dioxygenase III-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1184
Polymers29,9262
Non-polymers1922
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-65 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.851, 62.087, 98.055
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 Biphenyl-2,3-diol 1,2-dioxygenase III-related protein


Mass: 14963.179 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC_A0328, VC_A0341, VC_A0463 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIPL / References: UniProt: Q9K3D3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O

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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: 1.98 Å3/Da / Density % sol: 37.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 25% Peg 3350 0.2M LiSo4 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 7, 2008
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→26.23 Å / Num. obs: 27068 / % possible obs: 84.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.5 / Redundancy: 7 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 40.9
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 17.4 / Num. unique all: 1755 / Rsym value: 0.089 / % possible all: 38.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.automr)model building
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EY7

3ey7


Resolution: 1.6→26.228 Å / SU ML: 0.14 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 2602 5.14 %RANDOM
Rwork0.1563 ---
obs0.1579 27025 83.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.508 Å2 / ksol: 0.335 e/Å3
Refinement stepCycle: LAST / Resolution: 1.6→26.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 10 320 2400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6001-1.62920.2457660.1603922X-RAY DIFFRACTION31
1.6292-1.66050.2691550.14261167X-RAY DIFFRACTION39
1.6605-1.69440.1478940.13671431X-RAY DIFFRACTION48
1.6944-1.73130.1912850.15131773X-RAY DIFFRACTION59
1.7313-1.77150.18131040.14692281X-RAY DIFFRACTION74
1.7715-1.81580.17751450.15932784X-RAY DIFFRACTION93
1.8158-1.86490.21661530.15972771X-RAY DIFFRACTION92
1.8649-1.91980.20551750.16942812X-RAY DIFFRACTION94
1.9198-1.98170.23311500.162853X-RAY DIFFRACTION94
1.9817-2.05250.19531760.14632824X-RAY DIFFRACTION94
2.0525-2.13470.20341380.14852892X-RAY DIFFRACTION95
2.1347-2.23180.20321370.14592910X-RAY DIFFRACTION96
2.2318-2.34940.1821550.152893X-RAY DIFFRACTION96
2.3494-2.49640.19241380.15422945X-RAY DIFFRACTION96
2.4964-2.6890.17611600.16682919X-RAY DIFFRACTION97
2.689-2.95930.19781640.1712937X-RAY DIFFRACTION97
2.9593-3.38670.19041910.15612939X-RAY DIFFRACTION98
3.3867-4.2640.13771760.12912978X-RAY DIFFRACTION99
4.264-26.23160.16841400.15763022X-RAY DIFFRACTION99

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