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- PDB-3ct8: Crystal structure of a putative glyoxalase (NP_243026.1) from Bac... -

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Basic information

Entry
Database: PDB / ID: 3ct8
TitleCrystal structure of a putative glyoxalase (NP_243026.1) from Bacillus halodurans at 2.10 A resolution
ComponentsPutative glyoxalase
KeywordsLYASE / NP_243026.1 / Putative Glyoxalase / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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
Unknown ligand / BH2160 protein
Similarity search - Component
Biological speciesBacillus halodurans C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative Glyoxalase (NP_243026.1) from Bacillus halodurans at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative glyoxalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4493
Polymers17,3831
Non-polymers652
Water50428
1
A: Putative glyoxalase
hetero molecules

A: Putative glyoxalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8976
Polymers34,7662
Non-polymers1314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4290 Å2
ΔGint-18.5 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.380, 51.380, 116.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-134-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative glyoxalase / Protein BH2160


Mass: 17383.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans C-125 (bacteria) / Species: Bacillus halodurans / Strain: C-125 / DSM 18197 / FERM 7344 / JCM 9153 / Gene: NP_243026.1, BH2160 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9KAX6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 40.0% MPD, 5.0% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.92522, 0.97922, 0.97464
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.925221
20.979221
30.974641
ReflectionResolution: 2.09→26.528 Å / Num. obs: 9659 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 44.118 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.09-2.160.9021.648061296177.8
2.16-2.250.672.270681841199.6
2.25-2.350.5222.865731718199.5
2.35-2.480.357470641836199.6
2.48-2.630.2186.265981713199.9
2.63-2.830.1389.567461751199.9
2.83-3.120.07715.569861804199.9
3.12-3.570.04225.368171761199.9
3.57-4.490.02837.167931766199.9
4.49-26.5280.0234568741793198.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
XDSdata reduction
SHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→26.528 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.946 / SU B: 12.209 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.187
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. X-RAY FLUORESCENCE EXCITATION, WAVELENGTH SCANS AND ANOMALOUS DIFFERENCE FOURIERS SUPPORT THE MODELING OF ZN ION. 5. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED NEAR THE ZN ION SITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 461 4.8 %RANDOM
Rwork0.216 ---
obs0.217 9609 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.793 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--0.91 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 2.1→26.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 27 28 1148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211158
X-RAY DIFFRACTIONr_bond_other_d0.0030.02806
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.9471570
X-RAY DIFFRACTIONr_angle_other_deg1.55831951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3625134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.20723.38762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87915181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.773158
X-RAY DIFFRACTIONr_chiral_restr0.1090.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211278
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02251
X-RAY DIFFRACTIONr_mcbond_it1.2012665
X-RAY DIFFRACTIONr_mcbond_other0.2442269
X-RAY DIFFRACTIONr_mcangle_it2.18441071
X-RAY DIFFRACTIONr_scbond_it4.2316493
X-RAY DIFFRACTIONr_scangle_it6.1268498
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 42 -
Rwork0.279 647 -
all-689 -
obs--98.01 %
Refinement TLS params.Method: refined / Origin x: 21.841 Å / Origin y: 19.915 Å / Origin z: 22.591 Å
111213212223313233
T-0.039 Å20.0467 Å2-0.053 Å2-0.0047 Å2-0.0034 Å2---0.0627 Å2
L2.4062 °2-0.3084 °2-0.4505 °2-2.9662 °20.3058 °2--3.768 °2
S0.0118 Å °0.0419 Å °-0.1889 Å °-0.4884 Å °-0.0072 Å °0.1878 Å °-0.1238 Å °-0.7333 Å °-0.0045 Å °

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