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- PDB-5a8j: Crystal structure of the ArnB paralog VWA2 from Sulfolobus acidoc... -

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Basic information

Entry
Database: PDB / ID: 5a8j
TitleCrystal structure of the ArnB paralog VWA2 from Sulfolobus acidocaldarius
ComponentsVWA2
KeywordsTRANSCRIPTION / VON WILLEBRAND / PHOSPHORYLATION
Function / homologyArchaellum regulatory network B, C-terminal / Archaellum regulatory network B, C-terminal domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / CITRIC ACID / Conserved protein
Function and homology information
Biological speciesSULFOLOBUS ACIDOCALDARIUS (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.46 Å
AuthorsHoffmann, L. / Anders, K. / Reimann, J. / Linne, U. / Essen, L.-O. / Albers, S.-V.
CitationJournal: To be Published
Title: Phosphorylation-Dependent Interaction between an Archaeal Von Willebrand and Fha Domain Recruits Arna-Arnb Complex to DNA for Repression of Motility
Authors: Hoffmann, L. / Anders, K. / Reimann, J. / Linne, U. / Essen, L.-O. / Albers, S.-V.
History
DepositionJul 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VWA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,52310
Polymers41,7721
Non-polymers7509
Water5,819323
1
A: VWA2
hetero molecules

A: VWA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,04620
Polymers83,5452
Non-polymers1,50118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6540 Å2
ΔGint-90.1 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.640, 74.280, 145.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2185-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein VWA2


Mass: 41772.461 Da / Num. of mol.: 1 / Fragment: VON WILLEBRAND DOMAIN, RESIDUES 2-360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS ACIDOCALDARIUS (acidophilic)
Strain: DSM639 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA-PLYSS / References: UniProt: Q4J9H5

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Non-polymers , 6 types, 332 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.26 Å3/Da / Density % sol: 45.46 % / Description: NONE
Crystal growDetails: RESERVOIR BUFFER: 0.1 M SODIUMCITRATE PH 5.5; 2.5 M AMMONIUMSULFATE; PROTEIN BUFFER: 20 MM HEPES PH 7.0; 100 MM KCL, 2.7 MG/ML PROTEIN IN PROTEIN BUFFER; MIX RESERVOIR AND PROTEIN 1:1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.70847
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2011
RadiationMonochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70847 Å / Relative weight: 1
ReflectionResolution: 1.46→41.66 Å / Num. obs: 65094 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 16.79 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.5
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.5 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
CCP4phasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.46→41.658 Å / SU ML: 0.18 / σ(F): 1.37 / Phase error: 21.96 / Stereochemistry target values: ML
Details: RESIDUES A2 - G366 OF VWA2 CAN BE SEEN IN THE STRUCTURE
RfactorNum. reflection% reflection
Rfree0.2013 1340 2.1 %
Rwork0.1651 --
obs0.1659 65082 99.08 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 1.46→41.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2847 0 45 323 3215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113071
X-RAY DIFFRACTIONf_angle_d1.344201
X-RAY DIFFRACTIONf_dihedral_angle_d14.6041213
X-RAY DIFFRACTIONf_chiral_restr0.077504
X-RAY DIFFRACTIONf_plane_restr0.007536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4602-1.51240.29081340.22016129X-RAY DIFFRACTION97
1.5124-1.5730.24851220.21346367X-RAY DIFFRACTION100
1.573-1.64460.26831160.20216402X-RAY DIFFRACTION100
1.6446-1.73130.26671420.20096342X-RAY DIFFRACTION100
1.7313-1.83970.22891320.18886355X-RAY DIFFRACTION100
1.8397-1.98180.23951440.16246371X-RAY DIFFRACTION99
1.9818-2.18120.20121220.15536357X-RAY DIFFRACTION99
2.1812-2.49680.19541540.14856360X-RAY DIFFRACTION99
2.4968-3.14560.20441380.15336393X-RAY DIFFRACTION98
3.1456-41.67450.15721360.15896666X-RAY DIFFRACTION99

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