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- PDB-5h5w: Crystal structure of the flagellar cap protein FliD D2-D3 domains... -

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Basic information

Entry
Database: PDB / ID: 5h5w
TitleCrystal structure of the flagellar cap protein FliD D2-D3 domains from Escherichia coli
ComponentsFlagellar hook-associated protein 2
KeywordsSTRUCTURAL PROTEIN / Bacterial flagellar cap protein
Function / homology
Function and homology information


bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum-dependent cell motility / cell adhesion / extracellular region
Similarity search - Function
Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus
Similarity search - Domain/homology
: / Flagellar hook-associated protein 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSong, W.S. / Cho, S.Y. / Hong, H.J. / Yoon, S.I.
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Self-Oligomerizing Structure of the Flagellar Cap Protein FliD and Its Implication in Filament Assembly.
Authors: Song, W.S. / Cho, S.Y. / Hong, H.J. / Park, S.C. / Yoon, S.I.
History
DepositionNov 9, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
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: Flagellar hook-associated protein 2
B: Flagellar hook-associated protein 2


Theoretical massNumber of molelcules
Total (without water)41,4072
Polymers41,4072
Non-polymers00
Water2,522140
1
A: Flagellar hook-associated protein 2

A: Flagellar hook-associated protein 2

A: Flagellar hook-associated protein 2

A: Flagellar hook-associated protein 2

A: Flagellar hook-associated protein 2

A: Flagellar hook-associated protein 2


Theoretical massNumber of molelcules
Total (without water)124,2206
Polymers124,2206
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
crystal symmetry operation4_755-x+2,-y,z1
crystal symmetry operation5_665y+1,-x+y+1,z1
crystal symmetry operation6_545x-y,x-1,z1
2
B: Flagellar hook-associated protein 2

B: Flagellar hook-associated protein 2

B: Flagellar hook-associated protein 2

B: Flagellar hook-associated protein 2

B: Flagellar hook-associated protein 2

B: Flagellar hook-associated protein 2


Theoretical massNumber of molelcules
Total (without water)124,2206
Polymers124,2206
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
crystal symmetry operation4_755-x+2,-y,z1
crystal symmetry operation5_665y+1,-x+y+1,z1
crystal symmetry operation6_545x-y,x-1,z1
Unit cell
Length a, b, c (Å)118.326, 118.326, 59.581
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNGLNGLNAA104 - 22340 - 159
211GLNGLNGLNGLNBB104 - 22340 - 159
112ALAALAALAALAAA72 - 1038 - 39
212ALAALAALAALABB72 - 1038 - 39
122ASNASNTHRTHRAA224 - 265160 - 201
222ASNASNTHRTHRBB224 - 265160 - 201

NCS ensembles :
ID
1
2

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Components

#1: Protein Flagellar hook-associated protein 2 / HAP2 / Flagellar cap protein


Mass: 20703.316 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 71-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fliD, OO96_01215 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A178ST54, UniProt: P24216*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2.4 M ammonium sulfate, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 26548 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 36.3
Reflection shellResolution: 2.15→2.19 Å

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H5V

5h5v


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.204 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25737 1233 5 %RANDOM
Rwork0.21056 ---
obs0.21297 23259 93.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å2-0.89 Å20 Å2
2---1.77 Å20 Å2
3---2.66 Å2
Refinement stepCycle: 1 / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 0 140 2925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212796
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9373816
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0125390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80827.383107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.09515443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.317158
X-RAY DIFFRACTIONr_chiral_restr0.1030.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022044
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5971.51938
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08123117
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2393858
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4784.5699
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
11480medium positional0.170.5
22292medium positional0.180.5
11370loose positional0.335
22220loose positional0.335
11480medium thermal0.732
22292medium thermal0.62
11370loose thermal1.2810
22220loose thermal0.9810
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 91 -
Rwork0.277 1603 -
obs--88.64 %
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)
14.83111.29921.84482.54741.64124.7908-0.03710.15130.4966-0.1587-0.3090.5552-0.4271-0.32510.34610.17970.0459-0.00620.1821-0.02860.1392119.334-29.864-19.075
22.23342.3914-1.05125.04650.47722.84290.2783-0.35290.28890.3896-0.16380.1222-0.26660.1698-0.11460.1747-0.03080.03690.2031-0.05180.1189145.055-16.3813.819
33.92681.0864-0.51212.0852-0.31780.91-0.19080.2345-0.457-0.07750.1026-0.33080.09060.05470.08830.1597-0.0020.0510.1191-0.04270.0827153.673-33.586-13.973
42.63420.4017-0.05133.29440.2261.7626-0.0574-0.081-0.39830.0819-0.05250.05610.2076-0.12380.10990.0998-0.01190.04090.08550.00070.0742131.166-47.4155.182
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A70 - 103
2X-RAY DIFFRACTION1A224 - 267
3X-RAY DIFFRACTION2B72 - 103
4X-RAY DIFFRACTION2B224 - 267
5X-RAY DIFFRACTION3A104 - 223
6X-RAY DIFFRACTION4B104 - 223

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