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- PDB-5hxg: STM1697-FlhD complex -

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Basic information

Entry
Database: PDB / ID: 5hxg
TitleSTM1697-FlhD complex
Components
  • Flagellar transcriptional regulator FlhD
  • Uncharacterized protein STM1697
KeywordsTRANSCRIPTION / STM1697-FlhD / complex
Function / homology
Function and homology information


regulation of bacterial-type flagellum assembly / : / bacterial-type flagellum assembly / positive regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Flagellar transcriptional activator fold / Flagellar transcriptional activator FlhD / Flagellar transcriptional activator FlhD / Flagellar transcriptional activator FlhD superfamily / Flagellar transcriptional activator (FlhD) / EAL domain superfamily / EAL domain profile. / EAL domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Anti-FlhC(2)FlhD(4) factor YdiV / Flagellar transcriptional regulator FlhD / Flagellar transcriptional regulator FlhD / Anti-FlhC(2)FlhD(4) factor YdiV
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Infantis str. SARB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsLi, B. / Yuan, Z. / Qin, L. / Gu, L.
CitationJournal: To Be Published
Title: Crystal structure of STM1697-FlhD complex
Authors: Li, B. / Yue, Y. / Yuan, Z. / Zhang, F. / Liu, Y. / Li, P. / Song, N. / Li, Z. / Gu, L. / Qin, L.
History
DepositionJan 30, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein STM1697
B: Flagellar transcriptional regulator FlhD
C: Uncharacterized protein STM1697
D: Flagellar transcriptional regulator FlhD


Theoretical massNumber of molelcules
Total (without water)79,6134
Polymers79,6134
Non-polymers00
Water5,296294
1
A: Uncharacterized protein STM1697
B: Flagellar transcriptional regulator FlhD


Theoretical massNumber of molelcules
Total (without water)39,8062
Polymers39,8062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-19 kcal/mol
Surface area13510 Å2
MethodPISA
2
C: Uncharacterized protein STM1697
D: Flagellar transcriptional regulator FlhD


Theoretical massNumber of molelcules
Total (without water)39,8062
Polymers39,8062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-18 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.006, 61.006, 166.891
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Uncharacterized protein STM1697


Mass: 26506.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Infantis str. SARB27 (bacteria)
Gene: SEENIN0B_01477 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G4C3X3, UniProt: A0A6C8G6L7*PLUS
#2: Protein Flagellar transcriptional regulator FlhD


Mass: 13299.331 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Infantis str. SARB27 (bacteria)
Strain: SARB27 / Gene: flhD, SEENIN0B_01241 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G4C1X0, UniProt: A0A6C8G6W0*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 0.2M KCl, 0.01M MgCl2, 0.05M MES pH5.6, 5% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.998→50 Å / Num. obs: 47026 / % possible obs: 97 % / Redundancy: 5.6 % / Net I/σ(I): 23.11

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.998→38.309 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 21.35
RfactorNum. reflection% reflection
Rfree0.2061 1941 4.25 %
Rwork0.178 --
obs0.1791 45724 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.998→38.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 0 294 4670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074468
X-RAY DIFFRACTIONf_angle_d0.8326050
X-RAY DIFFRACTIONf_dihedral_angle_d13.6432662
X-RAY DIFFRACTIONf_chiral_restr0.055706
X-RAY DIFFRACTIONf_plane_restr0.006760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9977-2.04770.31771240.21722917X-RAY DIFFRACTION91
2.0477-2.1030.26671300.19523010X-RAY DIFFRACTION92
2.103-2.16490.22361320.19053020X-RAY DIFFRACTION95
2.1649-2.23480.19511480.18383058X-RAY DIFFRACTION95
2.2348-2.31460.20971390.17223124X-RAY DIFFRACTION97
2.3146-2.40730.25561370.18323134X-RAY DIFFRACTION97
2.4073-2.51680.20731400.18023161X-RAY DIFFRACTION98
2.5168-2.64950.25161380.17283196X-RAY DIFFRACTION98
2.6495-2.81540.17881390.17243141X-RAY DIFFRACTION99
2.8154-3.03270.21771380.17783229X-RAY DIFFRACTION99
3.0327-3.33780.20591530.17333196X-RAY DIFFRACTION100
3.3378-3.82040.19491480.16723209X-RAY DIFFRACTION100
3.8204-4.81180.19261330.16033203X-RAY DIFFRACTION100
4.8118-38.31630.19231420.20153185X-RAY DIFFRACTION99
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)
11.3999-0.14350.40451.3490.41070.88170.1105-0.0924-0.11190.0063-0.0387-0.10030.073-0.0095-0.00010.2580.00130.01590.2620.03980.283154.05543.898118.065
20.51540.4099-0.03090.4414-0.03270.24260.2760.187-0.0305-0.3873-0.12080.5035-0.1558-0.09090.05140.50010.1628-0.03330.40110.00950.323134.228349.5571-0.9014
31.5193-0.1426-0.16271.3186-0.48950.91430.0383-0.0570.0576-0.12350.04040.14190.0256-0.07330.00010.2355-0.0033-0.01720.2305-0.03170.250172.001368.746122.3784
40.05830.08410.03210.8030.13320.14430.081-0.4883-0.39550.14790.1522-0.24690.08890.17380.03080.29370.0355-0.03490.60960.0330.316286.873554.46241.2458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'

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