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- PDB-4es4: Crystal structure of YdiV and FlhD complex -

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Basic information

Entry
Database: PDB / ID: 4es4
TitleCrystal structure of YdiV and FlhD complex
Components
  • Flagellar transcriptional regulator FlhD
  • Putative cyclic di-GMP regulator CdgR
KeywordsTRANSCRIPTION / Flagellar regulation
Function / homology
Function and homology information


positive regulation of bacterial-type flagellum assembly / negative regulation of bacterial-type flagellum-dependent cell motility / bacterial-type flagellum assembly / transcription regulator complex / DNA-templated transcription / 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 / EAL domain / EAL domain superfamily / TIM Barrel / Alpha-Beta Barrel ...Flagellar transcriptional activator fold / Flagellar transcriptional activator FlhD / Flagellar transcriptional activator FlhD / Flagellar transcriptional activator FlhD superfamily / Flagellar transcriptional activator (FlhD) / EAL domain / EAL domain / EAL domain superfamily / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Flagellar transcriptional regulator FlhD / Putative anti-FlhC(2)FlhD(4) factor YdiV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLi, B. / Gu, L.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural insight of a concentration-dependent mechanism by which YdiV inhibits Escherichia coli flagellum biogenesis and motility
Authors: Li, B. / Li, N. / Wang, F. / Guo, L. / Huang, Y. / Liu, X. / Wei, T. / Zhu, D. / Liu, C. / Pan, H. / Xu, S. / Wang, H.W. / Gu, L.
History
DepositionApr 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references / Other
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cyclic di-GMP regulator CdgR
B: Flagellar transcriptional regulator FlhD
C: Putative cyclic di-GMP regulator CdgR
D: Flagellar transcriptional regulator FlhD
E: Putative cyclic di-GMP regulator CdgR
F: Flagellar transcriptional regulator FlhD
G: Putative cyclic di-GMP regulator CdgR
H: Flagellar transcriptional regulator FlhD


Theoretical massNumber of molelcules
Total (without water)161,6148
Polymers161,6148
Non-polymers00
Water00
1
A: Putative cyclic di-GMP regulator CdgR
B: Flagellar transcriptional regulator FlhD
G: Putative cyclic di-GMP regulator CdgR
H: Flagellar transcriptional regulator FlhD


Theoretical massNumber of molelcules
Total (without water)80,8074
Polymers80,8074
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-59 kcal/mol
Surface area25060 Å2
MethodPISA
2
C: Putative cyclic di-GMP regulator CdgR
D: Flagellar transcriptional regulator FlhD
E: Putative cyclic di-GMP regulator CdgR
F: Flagellar transcriptional regulator FlhD


Theoretical massNumber of molelcules
Total (without water)80,8074
Polymers80,8074
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8850 Å2
ΔGint-58 kcal/mol
Surface area25040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.486, 132.486, 145.685
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PHEPHEILEILEchain A and (resseq 15:31 or resseq 53:233 )AA15 - 3115 - 31
121THRTHRTHRTHRchain A and (resseq 15:31 or resseq 53:233 )AA53 - 23353 - 233
211PHEPHEILEILEchain C and (resseq 15:31 or resseq 53:233 )CC15 - 3115 - 31
221THRTHRTHRTHRchain C and (resseq 15:31 or resseq 53:233 )CC53 - 23353 - 233
311PHEPHEILEILEchain E and (resseq 15:31 or resseq 53:233 )EE15 - 3115 - 31
321THRTHRTHRTHRchain E and (resseq 15:31 or resseq 53:233 )EE53 - 23353 - 233
411PHEPHEILEILEchain G and (resseq 15:31 or resseq 53:233 )GG15 - 3115 - 31
421THRTHRTHRTHRchain G and (resseq 15:31 or resseq 53:233 )GG53 - 23353 - 233
112HISHISASPASPchain B and (resseq 2:81 )BB2 - 812 - 81
212HISHISASPASPchain D and (resseq 2:81 )DD2 - 812 - 81
312HISHISASPASPchain F and (resseq 2:81 )FF2 - 812 - 81
412HISHISASPASPchain H and (resseq 2:81 )HH2 - 812 - 81

NCS ensembles :
ID
1
2

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Components

#1: Protein
Putative cyclic di-GMP regulator CdgR / c-diGMP regulator


Mass: 27070.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: cdgR, ydiV, b1707, JW1697 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76204
#2: Protein
Flagellar transcriptional regulator FlhD


Mass: 13333.386 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: flhD, flbB, b1892, JW1881 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A8S9

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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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1M Na/K phosphate pH5.8, 6% PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97939 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2011
RadiationMonochromator: SAGITTALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 33268 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.9-3110.7485.0332580.748100
6.24-509.90.0573.1334590.0598.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3TLQ, 1G8E

3tlq

1g8e


Resolution: 2.9→39.165 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.36 / σ(F): 0 / Phase error: 29.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 1914 6.09 %RANDOM
Rwork0.2445 ---
all0.2469 31417 --
obs0.2469 31417 94.33 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.863 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso max: 180.97 Å2 / Biso mean: 82.2457 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--11.0281 Å2-0 Å20 Å2
2---11.0281 Å2-0 Å2
3---22.0563 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9074 0 0 0 9074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119270
X-RAY DIFFRACTIONf_angle_d1.36712586
X-RAY DIFFRACTIONf_dihedral_angle_d19.1043370
X-RAY DIFFRACTIONf_chiral_restr0.0911474
X-RAY DIFFRACTIONf_plane_restr0.0051606
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1586X-RAY DIFFRACTIONPOSITIONAL0.064
12C1586X-RAY DIFFRACTIONPOSITIONAL0.064
13E1586X-RAY DIFFRACTIONPOSITIONAL0.059
14G1586X-RAY DIFFRACTIONPOSITIONAL0.067
21B640X-RAY DIFFRACTIONPOSITIONAL0.059
22D640X-RAY DIFFRACTIONPOSITIONAL0.059
23F640X-RAY DIFFRACTIONPOSITIONAL0.064
24H640X-RAY DIFFRACTIONPOSITIONAL0.064
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8975-2.96990.37621220.32981784190682
2.9699-3.05020.39781270.3171961208889
3.0502-3.13990.37081320.32521979211189
3.1399-3.24120.37641310.29732000213191
3.2412-3.3570.37381370.29312093223095
3.357-3.49130.28351350.26822105224095
3.4913-3.65010.33211360.24522144228096
3.6501-3.84240.26781270.22272122224996
3.8424-4.08290.28231390.21592140227996
4.0829-4.39770.20621430.2022177232097
4.3977-4.83950.26231400.19512187232798
4.8395-5.53820.29841480.24082224237298
5.5382-6.97110.27411420.26652270241299
6.9711-39.16860.24551550.24242317247298

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