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- PDB-2rk0: Crystal structure of glyoxylase/bleomycin resistance protein/diox... -

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Basic information

Entry
Database: PDB / ID: 2rk0
TitleCrystal structure of glyoxylase/bleomycin resistance protein/dioxygenase domain from Frankia sp. EAN1pec
ComponentsGlyoxalase/Bleomycin resistance protein/dioxygenase domain
KeywordsOXIDOREDUCTASE / 11002z / Glyoxylase / Bleomycin resistance protein / dioxygenase domain / PSI-II / NewYork Structural GenomiX research consortium (NYSGRC) / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


dioxygenase activity
Similarity search - Function
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
Glyoxalase/bleomycin resistance protein/dioxygenase / :
Similarity search - Component
Biological speciesFrankia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsSugadev, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of glyoxylase/bleomycin resistance protein/dioxygenase domain from Frankia sp. EAN1pec.
Authors: Sugadev, R. / 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 1.2Feb 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 1.3Nov 6, 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/Bleomycin resistance protein/dioxygenase domain
B: Glyoxalase/Bleomycin resistance protein/dioxygenase domain


Theoretical massNumber of molelcules
Total (without water)30,4652
Polymers30,4652
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
MethodPISA
2
A: Glyoxalase/Bleomycin resistance protein/dioxygenase domain
B: Glyoxalase/Bleomycin resistance protein/dioxygenase domain

A: Glyoxalase/Bleomycin resistance protein/dioxygenase domain
B: Glyoxalase/Bleomycin resistance protein/dioxygenase domain


Theoretical massNumber of molelcules
Total (without water)60,9304
Polymers60,9304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area10040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.445, 69.445, 213.958
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Glyoxalase/Bleomycin resistance protein/dioxygenase domain


Mass: 15232.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Frankia sp. (bacteria) / Strain: EAN1pec / Gene: Franean1DRAFT_2373 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3W3Y2, UniProt: A8LBF3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 1.4M Sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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 12, 2007 / Details: Mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 20212 / Num. obs: 20212 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 32.6 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.2
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 11 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3 / Num. unique all: 1709 / % possible all: 86.5

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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: 2.04→39.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 52343.51 / 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
Rfree0.256 935 4.8 %RANDOM
Rwork0.215 ---
all0.234 20212 --
obs0.215 19369 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.0032 Å2 / ksol: 0.365371 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å23.14 Å20 Å2
2--1.41 Å20 Å2
3----2.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.04→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 0 138 2174
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d0.67
LS refinement shellResolution: 2.04→2.17 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 111 4 %
Rwork0.237 2631 -
obs--83.1 %
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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