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- PDB-3myd: Structure of the Cytoplasmic domain of FlhA from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 3myd
TitleStructure of the Cytoplasmic domain of FlhA from Helicobacter pylori
ComponentsFlagellar biosynthesis protein flhA
KeywordsPROTEIN TRANSPORT / FlhA / flagellar export / Type III secretion / cytoplasmic fragment
Function / homology
Function and homology information


bacterial-type flagellum assembly / protein secretion / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Flagellar biosynthesis protein FlhA / FHIPEP family, domain 1 / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Glutaredoxin ...Flagellar biosynthesis protein FlhA / FHIPEP family, domain 1 / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellar biosynthesis protein FlhA / Flagellar biosynthesis protein FlhA
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsMoore, S.A. / Jia, Y.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure of the cytoplasmic domain of the flagellar secretion apparatus component FlhA from Helicobacter pylori.
Authors: Moore, S.A. / Jia, Y.
History
DepositionMay 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar biosynthesis protein flhA


Theoretical massNumber of molelcules
Total (without water)40,9721
Polymers40,9721
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.193, 136.200, 107.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsmonomer

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Components

#1: Protein Flagellar biosynthesis protein flhA


Mass: 40972.363 Da / Num. of mol.: 1 / Fragment: Cytoplasmic Fragment, residues 373-732
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: CCUG 17874 / Gene: flbA, flhA, HP1041, jhp_0383 / Plasmid: PGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q9ZM40, UniProt: O06758*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: precipitant: 15% MME-PEG 5K, 100 mM Na Cacodylate pH 6.2-6.7, 0.2 M Ammonium Sulfate, 6-8% v/v isopropanol,, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934, 0.97882, 0.97907, 0.98166
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2009 / Details: mirrors
RadiationMonochromator: Silicon 111 crystal monochromator and sagittally focusing mirrors
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.978821
30.979071
40.981661
ReflectionResolution: 2.4→30 Å / Num. all: 20405 / Num. obs: 20380 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 29.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.386 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→29.65 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 1 / SU B: 17.612 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.317 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2647 1037 5.1 %RANDOM
Rwork0.22356 ---
obs0.22557 19217 100 %-
all-20405 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.098 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å20 Å2
2--0.96 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2692 0 0 65 2757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222729
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9923696
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6075347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14225.586111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90815514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6341513
X-RAY DIFFRACTIONr_chiral_restr0.0830.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211978
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_it0.7141.51735
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35122809
X-RAY DIFFRACTIONr_scbond_it2.1113994
X-RAY DIFFRACTIONr_scangle_it3.3243.5887
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 82 -
Rwork0.266 1390 -
obs--100 %
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)
14.04021.5113-1.76362.6179-0.65532.87650.3517-0.06760.75030.04810.04070.2792-0.4783-0.1906-0.39240.21710.05170.07790.0604-0.00890.315634.211755.614356.3119
21.68150.1485-0.31822.1881-2.4444.14710.1831-0.21790.1868-0.1474-0.219-0.07450.12630.33880.03590.0447-0.01040.03130.069-0.03990.053440.20740.536661.1064
32.99580.41650.6784.877-1.54452.9835-0.04890.28160.8177-0.05320.03410.134-0.66250.22530.01480.2116-0.03090.04310.09340.05760.255358.203757.757838.1084
43.160.38470.33831.82340.47395.47870.10050.2242-0.19180.0558-0.00970.32670.1809-0.3515-0.09080.0109-0.0033-0.00120.0429-0.00930.085652.458934.340638.4393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A394 - 470
2X-RAY DIFFRACTION2A471 - 540
3X-RAY DIFFRACTION3A541 - 626
4X-RAY DIFFRACTION4A627 - 732

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