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- PDB-3rri: Crystal structure of glyoxalase/bleomycin resistance protein/diox... -

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Basic information

Entry
Database: PDB / ID: 3rri
TitleCrystal structure of glyoxalase/bleomycin resistance protein/dioxygenase from Alicyclobacillus acidocaldarius
ComponentsGlyoxalase/bleomycin resistance protein/dioxygenase
KeywordsMETAL BINDING PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / metalloprotein
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
ACETATE ION / Glyoxalase/bleomycin resistance protein/dioxygenase
Similarity search - Component
Biological speciesAlicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMichalska, K. / Marshall, N. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of glyoxalase/bleomycin resistance protein/dioxygenase from Alicyclobacillus acidocaldarius
Authors: Michalska, K. / Marshall, N. / Clancy, S. / Joachimiak, A.
History
DepositionApr 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4114
Polymers33,2922
Non-polymers1182
Water2,918162
1
A: Glyoxalase/bleomycin resistance protein/dioxygenase
B: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules

A: Glyoxalase/bleomycin resistance protein/dioxygenase
B: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules

A: Glyoxalase/bleomycin resistance protein/dioxygenase
B: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules

A: Glyoxalase/bleomycin resistance protein/dioxygenase
B: Glyoxalase/bleomycin resistance protein/dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,64216
Polymers133,1708
Non-polymers4728
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area32680 Å2
ΔGint-74 kcal/mol
Surface area36110 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-14 kcal/mol
Surface area11600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.728, 104.728, 49.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Glyoxalase/bleomycin resistance protein/dioxygenase


Mass: 16646.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
Strain: DSM 446 / Gene: Aaci_2434 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: C8WSF5
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.05 Å3/Da / Density % sol: 39.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis/Tris propane:NaOH, 2.8 M sodium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2011 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
111.000H, 1.000K, L10.65
111.000K, 1.000H, -L20.35
ReflectionResolution: 1.5→50 Å / Num. all: 43462 / Num. obs: 43267 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 32
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2167 / % possible all: 99.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: different crystal form of the same protein that was solved by SAD

Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / SU B: 2.425 / SU ML: 0.07 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, protocol for twinned data
RfactorNum. reflection% reflectionSelection details
Rfree0.15911 1082 2.5 %according to the highest possible lattice symmetry
Rwork0.13504 ---
all0.13563 43211 --
obs0.13563 42129 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.261 Å2
Baniso -1Baniso -2Baniso -3
1--10.82 Å20 Å20 Å2
2---10.82 Å20 Å2
3---21.64 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 0 8 162 2458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222411
X-RAY DIFFRACTIONr_bond_other_d0.0010.021720
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9473255
X-RAY DIFFRACTIONr_angle_other_deg0.84834099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.07222.466146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60615409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1011526
X-RAY DIFFRACTIONr_chiral_restr0.0880.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02600
X-RAY DIFFRACTIONr_mcbond_it0.8491.51358
X-RAY DIFFRACTIONr_mcbond_other0.2431.5534
X-RAY DIFFRACTIONr_mcangle_it1.522193
X-RAY DIFFRACTIONr_scbond_it2.22731053
X-RAY DIFFRACTIONr_scangle_it3.5154.51062
LS refinement shellResolution: 1.498→1.537 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 77 -
Rwork0.229 3049 -
obs-3049 98.61 %

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