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- PDB-3oa4: CRYSTAL STRUCTURE OF hypothetical protein BH1468 from Bacillus ha... -

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Basic information

Entry
Database: PDB / ID: 3oa4
TitleCRYSTAL STRUCTURE OF hypothetical protein BH1468 from Bacillus halodurans C-125
Componentsglyoxalase
KeywordsLYASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / glyoxalase family / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


Methylmalonyl-CoA epimerase / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsMalashkevich, V.N. / Patskovsky, Y. / Garrett, S. / Foti, R. / Toro, R. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF hypothetical protein BH1468 from Bacillus halodurans C-125
Authors: Malashkevich, V.N. / Patskovsky, Y. / Garrett, S. / Foti, R. / Toro, R. / Seidel, R. / Almo, S.C.
History
DepositionAug 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4734
Polymers18,2201
Non-polymers2543
Water1,00956
1
A: glyoxalase
hetero molecules

A: glyoxalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9478
Polymers36,4402
Non-polymers5076
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4430 Å2
ΔGint-126 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.264, 63.264, 90.855
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-194-

HOH

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Components

#1: Protein glyoxalase / BH1468 protein


Mass: 18219.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BAB05187.1, BH1468 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q9KCV1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0 M ammonium sulfate, 0.1 M TRIS, 0.2 M lithium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 14255 / % possible obs: 99.9 % / Redundancy: 15.2 % / Rmerge(I) obs: 0.09 / Χ2: 0.803 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.94-1.9713.30.8966960.454100
1.97-2.0114.30.7956760.417100
2.01-2.0514.70.6647280.4100
2.05-2.0915.30.5536810.465100
2.09-2.1415.40.4946930.437100
2.14-2.1815.70.4156900.472100
2.18-2.2415.80.357040.474100
2.24-2.315.90.3196940.525100
2.3-2.3715.80.2927070.509100
2.37-2.4415.90.2466940.553100
2.44-2.5315.70.2167250.553100
2.53-2.6315.80.176980.65100
2.63-2.7515.70.1537050.75100
2.75-2.915.70.1287060.856100
2.9-3.0815.60.1087120.988100
3.08-3.3215.50.0927241.231100
3.32-3.6515.10.0897241.599100
3.65-4.1814.80.0777371.694100
4.18-5.2614.20.0637491.50699.6
5.26-5013.40.068121.45598.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 59.38 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.9 Å
Translation2.5 Å36.9 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→19.54 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2293 / WRfactor Rwork: 0.1969 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8488 / SU B: 6.967 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1396 / SU Rfree: 0.1355 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 703 5 %RANDOM
Rwork0.1958 ---
obs0.1976 14122 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 106.18 Å2 / Biso mean: 46.9393 Å2 / Biso min: 28.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.94→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1073 0 12 56 1141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221106
X-RAY DIFFRACTIONr_angle_refined_deg1.40821486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7375139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.63325.62548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5415215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.534155
X-RAY DIFFRACTIONr_chiral_restr0.1010.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021808
X-RAY DIFFRACTIONr_mcbond_it1.173.5687
X-RAY DIFFRACTIONr_mcangle_it4.593501108
X-RAY DIFFRACTIONr_scbond_it10.89950419
X-RAY DIFFRACTIONr_scangle_it1.3924.5377
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 49 -
Rwork0.225 944 -
all-993 -
obs--97.64 %
Refinement TLS params.Method: refined / Origin x: 17.1646 Å / Origin y: -8.7124 Å / Origin z: -14.7577 Å
111213212223313233
T0.0446 Å20.0132 Å2-0.0085 Å2-0.0225 Å2-0.0192 Å2--0.0333 Å2
L1.2162 °20.8994 °2-0.1353 °2-2.327 °2-0.4745 °2--1.5725 °2
S0.0961 Å °-0.0758 Å °0.0058 Å °0.253 Å °0.007 Å °-0.0307 Å °-0.1105 Å °0.0246 Å °-0.1031 Å °

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