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- PDB-4pav: Structure of hypothetical protein SA1046 from S. aureus. -

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Basic information

Entry
Database: PDB / ID: 4pav
TitleStructure of hypothetical protein SA1046 from S. aureus.
ComponentsGlyoxalase family protein
KeywordsUNKNOWN FUNCTION / hypothetical protein
Function / homology2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Roll / Alpha Beta / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsBattaile, K.P. / Mulichak, A. / Lam, R. / Lam, K. / Soloveychik, M. / Romanov, V. / Jones, K. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: To Be Published
Title: Structure of hypothetical protein SA1046 from S. aureus.
Authors: Battaile, K.P. / Mulichak, A. / Lam, R. / Lam, K. / Soloveychik, M. / Romanov, V. / Jones, K. / Pai, E.F. / Chirgadze, N.Y.
History
DepositionApr 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyoxalase family protein
B: Glyoxalase family protein
C: Glyoxalase family protein
D: Glyoxalase family protein
E: Glyoxalase family protein
F: Glyoxalase family protein


Theoretical massNumber of molelcules
Total (without water)100,3496
Polymers100,3496
Non-polymers00
Water1,910106
1
A: Glyoxalase family protein


Theoretical massNumber of molelcules
Total (without water)16,7251
Polymers16,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glyoxalase family protein


Theoretical massNumber of molelcules
Total (without water)16,7251
Polymers16,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glyoxalase family protein


Theoretical massNumber of molelcules
Total (without water)16,7251
Polymers16,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glyoxalase family protein


Theoretical massNumber of molelcules
Total (without water)16,7251
Polymers16,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glyoxalase family protein


Theoretical massNumber of molelcules
Total (without water)16,7251
Polymers16,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Glyoxalase family protein


Theoretical massNumber of molelcules
Total (without water)16,7251
Polymers16,7251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: Glyoxalase family protein
B: Glyoxalase family protein
C: Glyoxalase family protein
D: Glyoxalase family protein
E: Glyoxalase family protein
F: Glyoxalase family protein

A: Glyoxalase family protein
B: Glyoxalase family protein
C: Glyoxalase family protein
D: Glyoxalase family protein
E: Glyoxalase family protein
F: Glyoxalase family protein


Theoretical massNumber of molelcules
Total (without water)200,69812
Polymers200,69812
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area47050 Å2
ΔGint-318 kcal/mol
Surface area57450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.650, 96.650, 204.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Glyoxalase family protein


Mass: 16724.861 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D0K9R6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.3M Ammonium sulphate, 0.1M citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97947 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.3→204.12 Å / Num. obs: 49078 / % possible obs: 98.3 % / Redundancy: 20.5 % / Biso Wilson estimate: 58.12 Å2 / Net I/σ(I): 36.7

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 2.3→33.67 Å / Cor.coef. Fo:Fc: 0.9355 / Cor.coef. Fo:Fc free: 0.9164 / SU R Cruickshank DPI: 0.231 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.225 / SU Rfree Blow DPI: 0.18 / SU Rfree Cruickshank DPI: 0.184
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2439 4.98 %RANDOM
Rwork0.2013 ---
obs0.2025 48983 98.25 %-
Displacement parametersBiso mean: 65.72 Å2
Baniso -1Baniso -2Baniso -3
1--7.2973 Å20 Å20 Å2
2---7.2973 Å20 Å2
3---14.5946 Å2
Refine analyzeLuzzati coordinate error obs: 0.377 Å
Refinement stepCycle: 1 / Resolution: 2.3→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5989 0 0 106 6095
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016099HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.188226HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2158SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes222HARMONIC2
X-RAY DIFFRACTIONt_gen_planes847HARMONIC5
X-RAY DIFFRACTIONt_it6099HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion18.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion766SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6624SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2357 159 5.24 %
Rwork0.2195 2877 -
all0.2203 3036 -
obs--98.25 %
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)
10.4983-0.74810.80731.7274-0.25910.91790.3707-0.64770.19710.3979-0.18970.0839-0.41530.0281-0.181-0.0884-0.0299-0.00950.1163-0.1081-0.2323-53.658545.905958.8522
20.38285.0813-1.21648.4730.711200.2082-0.32570.45970.1719-0.13490.2518-0.1414-0.132-0.07330.12370.07050.01870.3067-0.1463-0.0389-58.123452.204566.8667
32.78180.13521.1376.95390.57475.95820.1493-0.26480.20170.1109-0.15450.0371-0.2739-0.51850.0052-0.26970.03180.03750.0675-0.036-0.2163-61.849543.463256.4851
43.7794-0.78743.21293.3702-1.12964.81480.1311-0.3714-0.44420.37210.11330.19440.4169-0.347-0.2445-0.0245-0.0835-0.03560.12590.0267-0.2385-55.479329.595269.9278
51.1143-0.4422-0.21762.93870.80930.00020.0930.12480.3605-0.1975-0.3007-0.27890.07230.05830.20770.02050.00830.02210.01350.0716-0.023-34.224949.654493.7643
60.43032.85740.313411.9624-1.98050-0.29160.01840.1050.1730.055-0.527-0.34210.38410.23660.1488-0.0981-0.03190.04340.06860.0874-23.304549.578395.8818
75.57582.3289-1.63314.5662-1.84733.7609-0.0622-0.35260.13290.2182-0.021-0.1776-0.1542-0.09340.0832-0.0286-0.0183-0.0399-0.12610.0503-0.2029-35.390847.8079102.411
81.256-0.2078-0.5162.62370.75535.03460.10820.1177-0.0971-0.0331-0.15310.15620.2742-0.44610.045-0.0156-0.0622-0.0214-0.06150.0384-0.1698-38.932130.466692.4713
93.56021.78110.44492.44750.05784.6132-0.09790.3392-0.4012-0.42430.02310.00870.2946-0.05080.07480.02740.1594-0.0087-0.0234-0.0631-0.0977-17.92326.96359.275
10-1.04173.696-1.15918.8886-3.06332.7396-0.0420.06970.127-0.3180.3515-0.1543-0.1660.0786-0.30950.14110.07530.03870.2628-0.069-0.0542-18.569731.936451.6632
117.93832.6926-3.84625.9358-1.680211.8655-0.13290.4438-0.9135-0.12760.4089-0.59250.41660.4992-0.276-0.07760.17380.0624-0.25-0.1527-0.1302-12.339923.859360.3481
127.6789-0.0547-4.03580.89870.5415.622-0.09220.1765-0.957-0.0099-0.0019-0.19621.1082-0.23410.09410.11010.0132-0.0685-0.2533-0.0517-0.1093-29.898918.694369.1553
131.9611.35461.25023.07120.97545.71640.00490.1206-0.22840.2636-0.35810.4516-0.4062-0.88720.3532-0.06440.1981-0.0038-0.0854-0.12570.0031-51.564673.560772.5614
141.3111-0.9469-0.25290.1758-7.10251.69-0.0058-0.2712-0.26130.22280.07730.16670.1909-0.2319-0.0715-0.06940.12570.00870.1385-0.06350.0484-52.737367.645179.3521
153.5901-0.24721.22067.4366-2.198410.82390.1328-0.18420.34560.1004-0.29230.09210.0135-0.58460.1595-0.12530.2654-0.0558-0.1257-0.0874-0.0779-50.67575.307470.8664
160.5903-2.25550.25117.27884.81848.0463-0.09990.22980.1959-0.6402-0.3570.506-0.6821-1.05280.4569-0.09920.2122-0.12810.0207-0.0958-0.0177-54.381373.115655.2844
170.838-0.4698-0.35971.4380.20861.92960.0744-0.0734-0.15610.0651-0.0031-0.08550.28090.3172-0.0713-0.26630.0023-0.0561-0.057-0.0474-0.2902-47.801934.039751.5144
185.2908-3.29674.5254-4.4524-4.54283.3899-0.0784-0.1289-0.23180.36170.0069-0.21150.60460.28750.07140.34680.12550.01010.2104-0.0275-0.0686-39.950429.517652.7934
195.8872-1.58321.25093.6335-0.164.8103-0.0012-0.0025-0.20830.2962-0.05840.04650.55710.05530.0596-0.0948-0.0337-0.0705-0.0482-0.0331-0.2793-53.471930.867652.9447
202.77621.64940.17883.5268-0.66782.06630.1098-0.05830.2605-0.0251-0.04970.2289-0.1032-0.1925-0.0602-0.1440.0086-0.00660.0475-0.0484-0.1498-52.455248.436742.8672
213.9606-1.9893-0.91344.4430.35221.15640.24780.23020.1881-0.2729-0.15880.1374-0.1912-0.4735-0.0891-0.03930.0327-0.03460.02790.0715-0.1683-44.303445.51489.298
225.3274-2.70671.454-0.26034.73392.98580.12690.3622-0.0427-0.3601-0.1450.3007-0.0998-0.76870.01810.03550.036-0.03220.1950.03950.0064-53.999548.061385.0268
232.72020.7951.19664.0576-0.02264.4770.0952-0.03-0.077-0.01920.09770.3884-0.0384-0.5122-0.1929-0.17060.00890.0376-0.02480.0235-0.1572-48.980943.832296.6864
241.51282.3415-0.30243.8221-0.89572.14730.0627-0.28210.56890.4038-0.06540.5405-0.4768-0.30020.00270.03550.09730.0489-0.08910.0149-0.0042-42.143462.855398.2287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|-6 - 24}
2X-RAY DIFFRACTION2{A|25 - 37}
3X-RAY DIFFRACTION3{A|38 - 71}
4X-RAY DIFFRACTION4{A|72 - 125}
5X-RAY DIFFRACTION5{B|-6 - 24}
6X-RAY DIFFRACTION6{B|25 - 37}
7X-RAY DIFFRACTION7{B|38 - 71}
8X-RAY DIFFRACTION8{B|72 - 125}
9X-RAY DIFFRACTION9{C|-1 - 24}
10X-RAY DIFFRACTION10{C|25 - 37}
11X-RAY DIFFRACTION11{C|38 - 71}
12X-RAY DIFFRACTION12{C|72 - 125}
13X-RAY DIFFRACTION13{D|-1 - 24}
14X-RAY DIFFRACTION14{D|25 - 38}
15X-RAY DIFFRACTION15{D|39 - 71}
16X-RAY DIFFRACTION16{D|72 - 125}
17X-RAY DIFFRACTION17{E|1 - 24}
18X-RAY DIFFRACTION18{E|25 - 37}
19X-RAY DIFFRACTION19{E|38 - 71}
20X-RAY DIFFRACTION20{E|72 - 125}
21X-RAY DIFFRACTION21{F|-6 - 24}
22X-RAY DIFFRACTION22{F|25 - 38}
23X-RAY DIFFRACTION23{F|39 - 71}
24X-RAY DIFFRACTION24{F|72 - 125}

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