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- PDB-3vcx: Crystal structure of a putative glyoxalase/bleomycin resistance p... -

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Basic information

Entry
Database: PDB / ID: 3vcx
TitleCrystal structure of a putative glyoxalase/bleomycin resistance protein from Rhodopseudomonas palustris CGA009
ComponentsGlyoxalase/Bleomycin resistance protein/dioxygenase domain
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ALPHA + BETA / DIHYDROXYBIPHENYL DIOXYGENASE / DIOXYGENASE FOLD / ANTIBIOTIC RESISTANCE PROTEINS FAMILY / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


dioxygenase activity
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #120 / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #110 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Glyoxalase/Bleomycin resistance protein/dioxygenase domain
Similarity search - Component
Biological speciesRhodopseudomonas palustris CGA009 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.39 Å
AuthorsStogios, P.J. / Chang, C. / Evdokimova, E. / Egorova, O. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a putative glyoxalase/bleomycin resistance protein from Rhodopseudomonas palustris CGA009
Authors: Stogios, P.J. / Chang, C. / Evdokimova, E. / Egorova, O. / Joachimiak, A. / Edwards, A.M. / Savchenko, A.
History
DepositionJan 4, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionJan 18, 2012ID: 3M2O
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Structure summary

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,85110
Polymers36,2972
Non-polymers1,5548
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.825, 67.918, 103.481
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsdimer is in the asymmetric unit

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Components

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


Mass: 18148.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic)
Strain: CGA009 / Gene: RPA0902 / Plasmid: P15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6NBC6
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 1.685768 Å3/Da / Density % sol: 27.036226 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2N AMMONIUM SULFATE, 2% PEG400, 0.1 M HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 4, 2009 / Details: mirrors
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 52153 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 5.9 % / Biso Wilson estimate: 11.27 Å2 / Rsym value: 0.068 / Net I/σ(I): 35.65
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.03 / Rsym value: 0.557 / % possible all: 68.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.39→33.959 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0.2 / Phase error: 15.93 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1858 1887 3.93 %random
Rwork0.1521 ---
obs0.1534 48015 95.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.122 Å2-0 Å20 Å2
2--3.0397 Å2-0 Å2
3---0.6336 Å2
Refinement stepCycle: LAST / Resolution: 1.39→33.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 70 306 2273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192057
X-RAY DIFFRACTIONf_angle_d2.2242789
X-RAY DIFFRACTIONf_dihedral_angle_d13.056779
X-RAY DIFFRACTIONf_chiral_restr0.131310
X-RAY DIFFRACTIONf_plane_restr0.011361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.43970.23841640.21633999X-RAY DIFFRACTION85
1.4397-1.49730.23651810.18934427X-RAY DIFFRACTION93
1.4973-1.56550.19741840.16014510X-RAY DIFFRACTION94
1.5655-1.6480.18881870.14444556X-RAY DIFFRACTION96
1.648-1.75130.16511880.13334613X-RAY DIFFRACTION96
1.7513-1.88650.18331920.12994675X-RAY DIFFRACTION97
1.8865-2.07630.16181930.13354742X-RAY DIFFRACTION98
2.0763-2.37670.18951960.14054768X-RAY DIFFRACTION99
2.3767-2.99410.18481970.15374836X-RAY DIFFRACTION99
2.9941-33.96910.18332050.16125002X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.09430.1624-0.14591.0594-0.08161.09880.01220.0049-0.1225-0.0076-0.0101-0.09870.12710.23320.01170-0.0118-0.00520.04410.00270.056610.885624.916268.793
21.28660.2502-0.91861.5264-0.55372.45560.13130.1070.0947-0.2351-0.072-0.0227-0.3825-0.0196-0.04170.12510.00460.01670.04880.00130.03247.593132.553951.9817
31.0738-0.0888-0.16811.242-0.07381.27550.00420.03750.0767-0.02540.0185-0.0573-0.2434-0.01340.0099-0.0132-0.00960.00420.0141-0.00710.0433.883741.081269.9712
42.73760.070.48581.2350.00182.5576-0.0464-0.0529-0.16760.22750.0348-0.10470.18610.25490.00470.10370.0233-0.01280.05260.00340.03637.709833.796787.0032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 3:79
2X-RAY DIFFRACTION2chain A and resid 80:124
3X-RAY DIFFRACTION3chain B and resid 3:79
4X-RAY DIFFRACTION4chain B and resid 80:124

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