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- PDB-4z04: Crystal structure of a probable lactoylglutathione lyase from Bru... -

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Basic information

Entry
Database: PDB / ID: 4z04
TitleCrystal structure of a probable lactoylglutathione lyase from Brucella melitensis in complex with glutathione
ComponentsGlyoxalase/Bleomycin resistance /Dioxygenase superfamily protein
KeywordsLYASE / SSGCID / Brucella melitensis / PROBABLE LACTOYLGLUTATHIONE LYASE / gutathione / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


dioxygenase activity / metal ion binding
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
GLUTATHIONE / Glyoxalase/Bleomycin resistance protein/dioxygenase domain
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a probable lactoylglutathione lyase from Brucella melitensis in complex with glutathione
Authors: Abendroth, J. / Clifton, M.C. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMar 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / reflns_shell / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all / _struct_keywords.text
Revision 1.2Sep 27, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn
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_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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyoxalase/Bleomycin resistance /Dioxygenase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0745
Polymers14,4651
Non-polymers6094
Water2,198122
1
A: Glyoxalase/Bleomycin resistance /Dioxygenase superfamily protein
hetero molecules

A: Glyoxalase/Bleomycin resistance /Dioxygenase superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,14910
Polymers28,9312
Non-polymers1,2188
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2650 Å2
ΔGint-17 kcal/mol
Surface area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.630, 39.500, 41.700
Angle α, β, γ (deg.)90.000, 116.290, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 14465.282 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (strain 2308) (bacteria)
Strain: 2308 / Gene: BAB1_1899, DK47_1237 / Plasmid: BrabA.17481.b.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YLQ3

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Non-polymers , 5 types, 126 molecules

#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Molecular Dimensions, Morpheus e4: 30mM each: Di-Ethyleneglycol, Tri-Ethyleneglycol, TetraEthyleneglycol, Penta-Ethyleneglycol; 100mM Imidazole/MES pH 6.5; 12.5% each MPD (racemic), PEG 1K, ...Details: Molecular Dimensions, Morpheus e4: 30mM each: Di-Ethyleneglycol, Tri-Ethyleneglycol, TetraEthyleneglycol, Penta-Ethyleneglycol; 100mM Imidazole/MES pH 6.5; 12.5% each MPD (racemic), PEG 1K, PEG 3350; BrabA.17481.b.B1.PS02324 at 21.7mg/ml with 8mM Gluathione; Cryo: direct; tray 261781e4; puck epp4-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 12, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 21619 / Num. obs: 21264 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.96 % / Biso Wilson estimate: 15.47 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.04 / Χ2: 1.012 / Net I/σ(I): 20.5 / Num. measured all: 84185
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.45-1.492.90.9140.3082.974138160114270.38389.1
1.49-1.530.960.2074.855163154615010.24697.1
1.53-1.570.9830.1616.786073149014890.18599.9
1.57-1.620.9860.1398.175946145214490.1699.8
1.62-1.670.9910.1110.345831142314170.12699.6
1.67-1.730.9930.09511.645600136313570.10999.6
1.73-1.80.9950.07814.275543134713460.0999.9
1.8-1.870.9970.06217.765184126112570.07199.7
1.87-1.960.9980.05121.95032122412190.05999.6
1.96-2.050.9980.04325.364828117011690.0599.9
2.05-2.160.9980.0428.734568112111120.04599.2
2.16-2.290.9990.03531.364369108010700.0499.1
2.29-2.450.9980.03533.7139709739690.0499.6
2.45-2.650.9990.03235.637319219230.037100
2.65-2.90.9990.03137.834448608480.03598.6
2.9-3.240.9990.02939.1931587827840.033100
3.24-3.740.9990.02641.6727196796730.0399.1
3.74-4.590.9990.02442.8224006015910.02798.3
4.59-6.480.9990.02441.4917604564510.02898.9
6.48-500.9980.02739.017282692120.03278.8

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
BALBESphasing
PHENIXmodel building
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QB5

4qb5


Resolution: 1.45→20.622 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1611 1082 5.09 %Random selectiob
Rwork0.1337 20174 --
obs0.1351 21256 98.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.37 Å2 / Biso mean: 25.2326 Å2 / Biso min: 12.51 Å2
Refinement stepCycle: final / Resolution: 1.45→20.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 37 122 1092
Biso mean--21.42 34.98 -
Num. residues----124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061030
X-RAY DIFFRACTIONf_angle_d1.021399
X-RAY DIFFRACTIONf_chiral_restr0.066137
X-RAY DIFFRACTIONf_plane_restr0.006187
X-RAY DIFFRACTIONf_dihedral_angle_d12.687355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.5160.18031370.14592327X-RAY DIFFRACTION92
1.516-1.59590.16261430.11562541X-RAY DIFFRACTION100
1.5959-1.69580.1581320.10892524X-RAY DIFFRACTION100
1.6958-1.82670.16671350.1122548X-RAY DIFFRACTION100
1.8267-2.01040.14341370.11592531X-RAY DIFFRACTION100
2.0104-2.3010.17171390.12542569X-RAY DIFFRACTION100
2.301-2.89770.17061300.15112549X-RAY DIFFRACTION100
2.8977-500.15461290.14182585X-RAY DIFFRACTION98

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