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- PDB-3bqx: High resolution crystal structure of a glyoxalase-related enzyme ... -

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Basic information

Entry
Database: PDB / ID: 3bqx
TitleHigh resolution crystal structure of a glyoxalase-related enzyme from Fulvimarina pelagi
ComponentsGlyoxalase-related enzyme
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / VOC superfamily / glyoxalase / Fulvimarina pelagi / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Glyoxalase-like domain / 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
VOC domain-containing protein
Similarity search - Component
Biological speciesFulvimarina pelagi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsRao, K.N. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: High resolution crystal structure of a glyoxalase-related enzyme from Fulvimarina pelagi.
Authors: Rao, K.N. / Burley, S.K. / Swaminathan, S.
History
DepositionDec 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
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 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Glyoxalase-related enzyme


Theoretical massNumber of molelcules
Total (without water)16,4301
Polymers16,4301
Non-polymers00
Water2,846158
1
A: Glyoxalase-related enzyme

A: Glyoxalase-related enzyme


Theoretical massNumber of molelcules
Total (without water)32,8602
Polymers32,8602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area5010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.930, 69.750, 83.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Glyoxalase-related enzyme


Mass: 16429.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fulvimarina pelagi (bacteria) / Strain: HTCC2506 / Gene: FP2506_05986 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0G7J9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.0M Ammonium sulfate, 10 mM Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9798 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 12, 2007 / Details: Diamond
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.32→17.07 Å / Num. all: 37108 / Num. obs: 37108 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.3
Reflection shellResolution: 1.32→1.39 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.861 / Mean I/σ(I) obs: 3.8 / Num. unique all: 5011 / % possible all: 92.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→17.07 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 686058.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / 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
Rfree0.248 1147 3.9 %RANDOM
Rwork0.238 ---
obs0.238 29094 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7993 Å2 / ksol: 0.37869 e/Å3
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2---0.94 Å20 Å2
3----0.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.4→17.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 0 158 1210
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.672
X-RAY DIFFRACTIONc_scbond_it2.42
X-RAY DIFFRACTIONc_scangle_it2.472.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 159 3.9 %
Rwork0.283 3941 -
obs--80 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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