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- PDB-4wia: Crystal structure of flagellar accessory protein FlaH from Methan... -

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Basic information

Entry
Database: PDB / ID: 4wia
TitleCrystal structure of flagellar accessory protein FlaH from Methanocaldococcus jannaschii
ComponentsPutative flagella-related protein H
KeywordsATP-BINDING PROTEIN / archaea / flagella
Function / homology
Function and homology information


archaeal-type flagellum / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
KaiC-like domain / KaiC / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Archaeal flagellar ATP-binding protein FlaH
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsMeshcheryakov, V.A. / Wolf, M.
CitationJournal: Protein Sci. / Year: 2016
Title: Crystal structure of the flagellar accessory protein FlaH of Methanocaldococcus jannaschii suggests a regulatory role in archaeal flagellum assembly.
Authors: Meshcheryakov, V.A. / Wolf, M.
History
DepositionSep 25, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

Deposited unit
A: Putative flagella-related protein H
B: Putative flagella-related protein H
C: Putative flagella-related protein H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,44717
Polymers79,1073
Non-polymers1,34114
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-240 kcal/mol
Surface area28430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.960, 130.960, 89.081
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
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA5 - 2335 - 233
21ALAALABB5 - 2335 - 233
12ILEILEAA5 - 2295 - 229
22ILEILECC5 - 2295 - 229
13ILEILEBB5 - 2295 - 229
23ILEILECC5 - 2295 - 229

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Putative flagella-related protein H


Mass: 26368.836 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Gene: flaH, MJ0899 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q58309
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 0.65 M Rb2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.97886, 0.97944
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 27, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978861
20.979441
ReflectionResolution: 2.2→50 Å / Num. obs: 45022 / % possible obs: 100 % / Redundancy: 10.6 % / Net I/σ(I): 11.9

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 15.644 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23296 2182 4.9 %RANDOM
Rwork0.20552 ---
obs0.20687 42807 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.069 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20.52 Å20 Å2
2--1.03 Å20 Å2
3----3.34 Å2
Refinement stepCycle: 1 / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5378 0 71 70 5519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195513
X-RAY DIFFRACTIONr_bond_other_d0.0070.025553
X-RAY DIFFRACTIONr_angle_refined_deg1.8542.0147442
X-RAY DIFFRACTIONr_angle_other_deg1.418312789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8975681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.81324.366213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.041151012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0831530
X-RAY DIFFRACTIONr_chiral_restr0.0930.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025978
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021146
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_it2.3263.1642732
X-RAY DIFFRACTIONr_mcbond_other2.3243.1632731
X-RAY DIFFRACTIONr_mcangle_it3.4964.7363411
X-RAY DIFFRACTIONr_mcangle_other3.4954.7383412
X-RAY DIFFRACTIONr_scbond_it2.9773.4582778
X-RAY DIFFRACTIONr_scbond_other2.9773.4572778
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4165.0814032
X-RAY DIFFRACTIONr_long_range_B_refined7.37325.3216061
X-RAY DIFFRACTIONr_long_range_B_other7.37925.3196061
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)
11A140960.14
12B140960.14
21A141570.13
22C141570.13
31B136060.16
32C136060.16
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 165 -
Rwork0.3 3127 -
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)
12.2997-0.2-0.48783.46780.86094.64270.0232-0.3045-0.38680.0674-0.0164-0.10950.41420.3612-0.00680.1819-0.16150.01810.31030.01040.07817.5445-71.4278109.8367
22.40710.7428-0.31923.7417-0.3491.63560.0360.01420.4003-0.0243-0.05830.7007-0.3776-0.76160.02230.39440.1460.09320.647-0.06390.3419-1.1434-37.655106.3397
32.43690.7072-0.38442.9784-1.16635.3432-0.00940.10580.04340.0099-0.0270.154-0.2214-0.23460.03640.1544-0.09650.00550.2891-0.00240.011120.0487-51.225576.547
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 233
2X-RAY DIFFRACTION2B5 - 233
3X-RAY DIFFRACTION3C5 - 230

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