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- PDB-4p94: The crystal structure of the soluble domain of Sulfolobus acidoca... -

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Basic information

Entry
Database: PDB / ID: 4p94
TitleThe crystal structure of the soluble domain of Sulfolobus acidocaldarius FlaF (residues 35-164)
ComponentsConserved flagellar protein F
KeywordsMOTOR PROTEIN / Immunoglobulin-like beta-sandwich
Function / homology: / Conserved flagellar protein F, immunoglobulin-like domain / identical protein binding / membrane / Conserved flagellar protein F
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 Å
AuthorsTsai, C.-L. / Arvai, A.S. / Ishida, J.P. / Tainer, J.A.
CitationJournal: Structure / Year: 2015
Title: FlaF Is a beta-Sandwich Protein that Anchors the Archaellum in the Archaeal Cell Envelope by Binding the S-Layer Protein.
Authors: Banerjee, A. / Tsai, C.L. / Chaudhury, P. / Tripp, P. / Arvai, A.S. / Ishida, J.P. / Tainer, J.A. / Albers, S.V.
History
DepositionApr 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved flagellar protein F
B: Conserved flagellar protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5213
Polymers32,4982
Non-polymers231
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.257, 127.257, 127.257
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-357-

HOH

21A-405-

HOH

31B-217-

HOH

41B-223-

HOH

51B-230-

HOH

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Components

#1: Protein Conserved flagellar protein F


Mass: 16248.860 Da / Num. of mol.: 2 / Fragment: UNP residues 35-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: Saci_1175 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4J9K8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 58.56 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 35% Tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.52→44.96 Å / Num. obs: 52512 / % possible obs: 100 % / Redundancy: 37.9 % / Biso Wilson estimate: 21.21 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.01 / Net I/σ(I): 33.6 / Num. measured all: 1992238 / Scaling rejects: 45
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.52-1.55300.022842.47773225930.425100
8.33-44.9656.30.036127.7200473560.00599.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA0.1.27data scaling
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4LIO

4lio
PDB Unreleased entry


Resolution: 1.651→44.96 Å / FOM work R set: 0.872 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1999 2067 5.02 %
Rwork0.1727 39080 -
obs0.174 41147 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.21 Å2 / Biso mean: 24.41 Å2 / Biso min: 12.73 Å2
Refinement stepCycle: final / Resolution: 1.651→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 1 234 2161
Biso mean--37.64 32.09 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072006
X-RAY DIFFRACTIONf_angle_d1.0622779
X-RAY DIFFRACTIONf_chiral_restr0.045336
X-RAY DIFFRACTIONf_plane_restr0.007352
X-RAY DIFFRACTIONf_dihedral_angle_d12.698711
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.651-1.68930.24271450.210325762721
1.6893-1.73150.22821480.204525782726
1.7315-1.77830.23391610.198625762737
1.7783-1.83070.2331370.198225512688
1.8307-1.88980.23511270.20826002727
1.8898-1.95730.25421280.222626062734
1.9573-2.03570.22221310.186425932724
2.0357-2.12830.20691510.17225762727
2.1283-2.24050.23611330.189226182751
2.2405-2.38090.22821340.201125742708
2.3809-2.56470.22761350.19226322767
2.5647-2.82280.22271300.196126122742
2.8228-3.23110.19161320.183726092741
3.2311-4.07050.18141500.144526452795
4.0705-45.00880.14091250.129327342859

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