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- PDB-5k5y: Crystal structure of truncated FlgD (monoclinic form) from the hu... -

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Basic information

Entry
Database: PDB / ID: 5k5y
TitleCrystal structure of truncated FlgD (monoclinic form) from the human pathogen Helicobacter pylori (strain 26695)
ComponentsBasal-body rod modification protein FlgD
KeywordsMOTOR PROTEIN / flagellin component D
Function / homology
Function and homology information


bacterial-type flagellum organization
Similarity search - Function
Immunoglobulin-like - #4070 / Flagellar hook capping protein / Flagellar hook capping protein - N-terminal region / FlgD Ig-like domain / FlgD Ig-like domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Basal-body rod modification protein FlgD
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsKekez, I. / Cendron, L. / Stojanovic, M. / Zanotti, G. / Matkovic-Calogovic, D.
Funding support Italy, 1items
OrganizationGrant numberCountry
University of PaduaPRIN 2010-2011 (MIUR) Italy
CitationJournal: Croatica Chemica Acta / Year: 2016
Title: Structure and Stability of FlgD from the Pathogenic 26695 Strain of Helicobacter pylori
Authors: Kekez, I. / Cendron, L. / Stojanovic, M. / Zanotti, G. / Matkovic-Calogovic, D.
History
DepositionMay 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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: Basal-body rod modification protein FlgD
B: Basal-body rod modification protein FlgD
C: Basal-body rod modification protein FlgD
D: Basal-body rod modification protein FlgD


Theoretical massNumber of molelcules
Total (without water)65,7944
Polymers65,7944
Non-polymers00
Water30617
1
A: Basal-body rod modification protein FlgD
B: Basal-body rod modification protein FlgD

A: Basal-body rod modification protein FlgD
B: Basal-body rod modification protein FlgD


Theoretical massNumber of molelcules
Total (without water)65,7944
Polymers65,7944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
D: Basal-body rod modification protein FlgD

C: Basal-body rod modification protein FlgD

C: Basal-body rod modification protein FlgD

D: Basal-body rod modification protein FlgD


Theoretical massNumber of molelcules
Total (without water)65,7944
Polymers65,7944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation2_656-x+1,y,-z+11
3
C: Basal-body rod modification protein FlgD

C: Basal-body rod modification protein FlgD

D: Basal-body rod modification protein FlgD

D: Basal-body rod modification protein FlgD


Theoretical massNumber of molelcules
Total (without water)65,7944
Polymers65,7944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
crystal symmetry operation1_454x-1,y,z-11
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)77.510, 34.000, 133.340
Angle α, β, γ (deg.)90.00, 98.90, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 127 - 272 / Label seq-ID: 1 - 146

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Basal-body rod modification protein FlgD


Mass: 16448.518 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: HP_0907 / Production host: Escherichia coli (E. coli) / References: UniProt: O25565
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: PEG 1500, succinic acid, sodium dihydrogen phosphate, glycine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.99988 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 2.8→76.58 Å / Num. obs: 16477 / % possible obs: 94.8 % / Redundancy: 2.7 % / Net I/σ(I): 4.9
Reflection shellHighest resolution: 2.8 Å / Rmerge(I) obs: 0.586

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLM7.2.1.data reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZZK

4zzk


Resolution: 2.85→62.16 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.914 / SU B: 20.558 / SU ML: 0.365 / Cross valid method: THROUGHOUT / ESU R Free: 0.424 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25561 798 5.1 %RANDOM
Rwork0.22678 ---
obs0.22825 14806 93.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.249 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.01 Å2
2--0.09 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.85→62.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4624 0 0 17 4641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194708
X-RAY DIFFRACTIONr_bond_other_d0.0070.024496
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9676324
X-RAY DIFFRACTIONr_angle_other_deg1.425310424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9635580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.23626.379232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93615888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4361512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215380
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021024
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_it5.4036.6182332
X-RAY DIFFRACTIONr_mcbond_other5.4036.6162331
X-RAY DIFFRACTIONr_mcangle_it8.6849.9052908
X-RAY DIFFRACTIONr_mcangle_other8.6829.9082909
X-RAY DIFFRACTIONr_scbond_it5.4767.0942376
X-RAY DIFFRACTIONr_scbond_other5.4757.0962377
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.09610.3813417
X-RAY DIFFRACTIONr_long_range_B_refined15.11161.25918530
X-RAY DIFFRACTIONr_long_range_B_other15.11161.26418530
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A170620.09
12B170620.09
21A169100.1
22C169100.1
31A169500.09
32D169500.09
41B167920.1
42C167920.1
51B168080.1
52D168080.1
61C169460.09
62D169460.09
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 50 -
Rwork0.386 1051 -
obs--92.91 %

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