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- PDB-3hnq: Crystal Structure of Virulence protein STM3117 from Salmonella ty... -

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Basic information

Entry
Database: PDB / ID: 3hnq
TitleCrystal Structure of Virulence protein STM3117 from Salmonella typhimurium. Northeast Structural Genomics Consortium target id StR274
ComponentsVirulence protein STM3117
KeywordsVIRAL PROTEIN / Virulence protein STM3117 / Salmonella typhimurium / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Virulence
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
Virulence protein STM3117
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSeetharaman, J. / Su, M. / Sahdev, S. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. / Montelione, G.T. ...Seetharaman, J. / Su, M. / Sahdev, S. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Virulence protein STM3117 from Salmonella typhimurium. Northeast Structural Genomics Consortium target id StR274
Authors: Seetharaman, J. / Su, M. / Sahdev, S. / Janjua, H. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMay 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Virulence protein STM3117
B: Virulence protein STM3117
C: Virulence protein STM3117
D: Virulence protein STM3117


Theoretical massNumber of molelcules
Total (without water)65,4004
Polymers65,4004
Non-polymers00
Water3,945219
1
A: Virulence protein STM3117


Theoretical massNumber of molelcules
Total (without water)16,3501
Polymers16,3501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Virulence protein STM3117


Theoretical massNumber of molelcules
Total (without water)16,3501
Polymers16,3501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Virulence protein STM3117


Theoretical massNumber of molelcules
Total (without water)16,3501
Polymers16,3501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Virulence protein STM3117


Theoretical massNumber of molelcules
Total (without water)16,3501
Polymers16,3501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Virulence protein STM3117
B: Virulence protein STM3117


Theoretical massNumber of molelcules
Total (without water)32,7002
Polymers32,7002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-19 kcal/mol
Surface area10770 Å2
MethodPISA
6
C: Virulence protein STM3117
D: Virulence protein STM3117


Theoretical massNumber of molelcules
Total (without water)32,7002
Polymers32,7002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-20 kcal/mol
Surface area11070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.950, 134.623, 51.356
Angle α, β, γ (deg.)90.00, 112.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Virulence protein STM3117


Mass: 16350.045 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: STM3117 / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZM36
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 36.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 1000, 100mM Na3Citrate, 100mm K2HPo4, 20% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 62170 / Num. obs: 62170 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.078
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2 % / Rmerge(I) obs: 0.43 / % possible all: 74

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→47.37 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 72554.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2658 5 %RANDOM
Rwork0.215 ---
obs0.215 53582 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.3194 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20.75 Å2
2--0.34 Å20 Å2
3----1.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.1→47.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3914 0 0 219 4133
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.37
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 351 4.8 %
Rwork0.29 7029 -
obs--76.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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