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- PDB-4zbh: THE CRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF SULFOLOBUS ACIDOCA... -

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Basic information

Entry
Database: PDB / ID: 4zbh
TitleTHE CRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF SULFOLOBUS ACIDOCALDARIUS FLAF
ComponentsConserved flagellar protein F
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN-LIKE BETA-SANDWICH / stator protein
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 / SIRAS / Resolution: 1.5 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 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved flagellar protein F


Theoretical massNumber of molelcules
Total (without water)16,2491
Polymers16,2491
Non-polymers00
Water3,099172
1
A: Conserved flagellar protein F

A: Conserved flagellar protein F


Theoretical massNumber of molelcules
Total (without water)32,4982
Polymers32,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area1020 Å2
ΔGint-9 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.407, 52.407, 100.241
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsDimer according to SAXS and gel filtration

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Components

#1: Protein Conserved flagellar protein F


Mass: 16248.860 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: Saci_1175 / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: Q4J9K8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3 M POTASSIUM CHLORIDE AND 50 mM HEPES, PH7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.9677 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 22800 / % possible obs: 98.4 % / Redundancy: 5.6 % / Rsym value: 0.051 / Net I/σ(I): 62.6
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 3.7 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.5→46.44 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 1082 4.99 %
Rwork0.158 --
obs0.16 21699 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms929 0 0 174 1103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005954
X-RAY DIFFRACTIONf_angle_d1.0421317
X-RAY DIFFRACTIONf_dihedral_angle_d12.529332
X-RAY DIFFRACTIONf_chiral_restr0.068159
X-RAY DIFFRACTIONf_plane_restr0.006165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4997-1.5680.25241120.16392209X-RAY DIFFRACTION83
1.568-1.65070.25861320.13642430X-RAY DIFFRACTION90
1.6507-1.75410.20271330.12342507X-RAY DIFFRACTION93
1.7541-1.88950.17641300.1192540X-RAY DIFFRACTION93
1.8895-2.07970.16361330.1162577X-RAY DIFFRACTION95
2.0797-2.38060.18111430.13342679X-RAY DIFFRACTION97
2.3806-2.99920.22711430.17762724X-RAY DIFFRACTION98
2.9992-46.46510.1911560.17552951X-RAY DIFFRACTION100

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