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- PDB-2rk9: The crystal structure of a glyoxalase/bleomycin resistance protei... -

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Basic information

Entry
Database: PDB / ID: 2rk9
TitleThe crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase superfamily member from Vibrio splendidus 12B01
ComponentsGlyoxalase/bleomycin resistance protein/dioxygenase
KeywordsOXIDOREDUCTASE / 11005r / Glyoxalase/bleomycin resistance protein/dioxygenase superfamily / NYSGXRC / Structural Genomics / Protein Structure Initiative II / New York SGX Research Center for Structural Genomics / PSI-2
Function / homology2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / dioxygenase activity / Roll / Alpha Beta / Glyoxalase/bleomycin resistance protein/dioxygenase
Function and homology information
Biological speciesVibrio splendidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsTyagi, R. / Eswaramoorthy, S. / Sauder, J.M. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase superfamily member from Vibrio splendidus 12B01.
Authors: Tyagi, R. / Eswaramoorthy, S. / Sauder, J.M. / Burley, S.K. / Swaminathan, S.
History
DepositionOct 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Glyoxalase/bleomycin resistance protein/dioxygenase
B: Glyoxalase/bleomycin resistance protein/dioxygenase


Theoretical massNumber of molelcules
Total (without water)33,7092
Polymers33,7092
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.704, 76.954, 42.395
Angle α, β, γ (deg.)90.00, 92.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glyoxalase/bleomycin resistance protein/dioxygenase


Mass: 16854.396 Da / Num. of mol.: 2 / Mutation: I119M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio splendidus (bacteria) / Strain: 12B01 / Gene: 84385607, V12B01_25774 / Plasmid: pSGX3-BC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A3UM69
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 1.97 Å3/Da / Density % sol: 37.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M NaCl, 0.1 M Sodium acetate pH 4.6, 30% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2007 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 32833 / Num. obs: 32833 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2274 / % possible all: 65.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→40.68 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 107646.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1304 4 %RANDOM
Rwork0.209 ---
obs0.209 32395 93.9 %-
all-32833 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.3429 Å2 / ksol: 0.399467 e/Å3
Displacement parametersBiso mean: 14.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å2-1.51 Å2
2---0.28 Å20 Å2
3----0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.6→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 0 218 2123
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.238 173 4.3 %
Rwork0.218 3847 -
obs--69.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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