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- PDB-1xqa: Structure of a possible Glyoxalase from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 1xqa
TitleStructure of a possible Glyoxalase from Bacillus cereus
ComponentsGlyoxalase/Bleomycin resistance protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Dioxygenase / Glyoxalase/Bleomycin resistance / Midwest Center for Structural Genomics / MCSG / Protein Structure Initiative / PSI
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
VOC domain-containing protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsCuff, M.E. / Li, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of a possible Glyoxalase from Bacillus cereus
Authors: Cuff, M.E. / Li, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Remark 600HETEROGEN THE LIGAND LABELED P6G IS TECHNICALLY FRAGMENTS OF PEG MME 550.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyoxalase/Bleomycin resistance protein
B: Glyoxalase/Bleomycin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1135
Polymers25,7822
Non-polymers3313
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glyoxalase/Bleomycin resistance protein
hetero molecules

A: Glyoxalase/Bleomycin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1135
Polymers25,7822
Non-polymers3313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area3690 Å2
ΔGint-43 kcal/mol
Surface area11170 Å2
MethodPISA
3
A: Glyoxalase/Bleomycin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1983
Polymers12,8911
Non-polymers3072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
B: Glyoxalase/Bleomycin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9152
Polymers12,8911
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)43.535, 61.616, 78.382
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 Glyoxalase/Bleomycin resistance protein / hypothetical protein BC3580


Mass: 12891.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Species: Bacillus cereus / Strain: ATCC 14579 / DSM 31 / Gene: AAP10513 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q81AI8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.1 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG MME 550, NaCl, BisTris, glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.980141 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: May 30, 2004 / Details: SBC3
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980141 Å / Relative weight: 1
ReflectionResolution: 1.8→38.06 Å / Num. all: 19959 / Num. obs: 19959 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Net I/σ(I): 6.5
Reflection shellResolution: 1.81→1.89 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.372 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
SHELXDphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→48.45 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.307 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.159 / ESU R Free: 0.146
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23552 1024 5.1 %RANDOM
Rwork0.18925 ---
all0.224 18935 --
obs0.19155 18935 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.358 Å2
Baniso -1Baniso -2Baniso -3
1-3.32 Å20 Å20 Å2
2---0.93 Å20 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 21 302 2084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221892
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.9742555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8515235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42124.38289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53315323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.953159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021451
X-RAY DIFFRACTIONr_nbd_refined0.1960.2878
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21307
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2219
X-RAY DIFFRACTIONr_metal_ion_refined0.0540.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.242
X-RAY DIFFRACTIONr_mcbond_it0.961.51183
X-RAY DIFFRACTIONr_mcangle_it1.37221861
X-RAY DIFFRACTIONr_scbond_it2.2263787
X-RAY DIFFRACTIONr_scangle_it3.5034.5694
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 72 -
Rwork0.22 1299 -
obs--93.46 %
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)
10.90920.2691-0.21880.7498-0.11571.5454-0.0487-0.0585-0.00450.01650.0072-0.0317-0.02420.04030.0415-0.04920.0202-0.0123-0.03130.0096-0.02613.05877.656217.804
20.80790.4018-0.04380.88740.13851.01860.0375-0.0246-0.0215-0.0114-0.0399-0.01020.0190.03310.0023-0.03990.01510.0024-0.03820.0082-0.025418.7918-1.3821-4.2668
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1121 - 113
2X-RAY DIFFRACTION2BB1 - 1122 - 113

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