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- PDB-4zzk: Crystal structure of truncated FlgD (monoclinic form) from the hu... -

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Basic information

Entry
Database: PDB / ID: 4zzk
TitleCrystal structure of truncated FlgD (monoclinic form) from the human pathogen Helicobacter pylori
ComponentsBasal-body rod modification protein FlgD
KeywordsMOTOR PROTEIN / Flagellum / Hook-caping protein
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: 2.75 Å
AuthorsPulic, I. / Cendron, L. / Salamina, M. / Matkovic-Calogovic, D. / Zanotti, G.
Funding support Italy, Croatia, 3items
OrganizationGrant numberCountry
European Community's Seventh Framework Program (FP7/2007-2013)283570 Italy
PRIN 2010-2011 (MIUR) Italy
Ministry of Science, Education and Sports119-1193079-1084 Croatia
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Crystal structure of truncated FlgD from the human pathogen Helicobacter pylori.
Authors: Pulic, I. / Cendron, L. / Salamina, M. / Polverino de Laureto, P. / Matkovic-Calogovic, D. / Zanotti, G.
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jan 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)65,8544
Polymers65,8544
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-7 kcal/mol
Surface area32520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.420, 34.220, 131.640
Angle α, β, γ (deg.)90.00, 99.58, 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: 0 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / 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: 16463.596 Da / Num. of mol.: 4 / Fragment: UNP residues 127-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: flgD, HPG27_858 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5Z7R3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 53 % / Description: Prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: SPG,PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.75→54.09 Å / Num. obs: 18375 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.077 / Rsym value: 0.047 / Net I/σ(I): 14.4
Reflection shellResolution: 2.75→2.88 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZZF

4zzf


Resolution: 2.75→38.39 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.896 / SU B: 16.528 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27487 1838 10 %RANDOM
Rwork0.22067 ---
obs0.22599 16537 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.351 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2--0.07 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.75→38.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4628 0 0 44 4672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194712
X-RAY DIFFRACTIONr_bond_other_d0.0070.024524
X-RAY DIFFRACTIONr_angle_refined_deg1.491.976324
X-RAY DIFFRACTIONr_angle_other_deg1.432310496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5515580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33726.316228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62415900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9061512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215356
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021016
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_it4.9465.9312332
X-RAY DIFFRACTIONr_mcbond_other4.9365.9292331
X-RAY DIFFRACTIONr_mcangle_it7.9568.8762908
X-RAY DIFFRACTIONr_mcangle_other7.9558.8782909
X-RAY DIFFRACTIONr_scbond_it4.8286.4042380
X-RAY DIFFRACTIONr_scbond_other4.8276.4062381
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.979.3443417
X-RAY DIFFRACTIONr_long_range_B_refined13.5954.87518421
X-RAY DIFFRACTIONr_long_range_B_other13.58954.87518419
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)
11A171520.08
12B171520.08
21A171420.09
22C171420.09
31A170200.09
32D170200.09
41B171700.08
42C171700.08
51B171680.09
52D171680.09
61C170080.1
62D170080.1
LS refinement shellResolution: 2.746→2.817 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 133 -
Rwork0.348 1195 -
obs--98.3 %

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