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- PDB-5a8i: Crystal structure of the FHA domain of ArnA from Sulfolobus acido... -

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Basic information

Entry
Database: PDB / ID: 5a8i
TitleCrystal structure of the FHA domain of ArnA from Sulfolobus acidocaldarius
ComponentsARNA
KeywordsTRANSCRIPTION / ZINC BINDING PROTEIN / FHA / ARCHAEA / REGULATION / MOTILITY
Function / homology
Function and homology information


Zinc-ribbon domain / zinc-ribbon domain / : / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Zinc finger RanBP2 type profile. ...Zinc-ribbon domain / zinc-ribbon domain / : / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSULFOLOBUS ACIDOCALDARIUS (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_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

Downloads & links

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Assembly

Deposited unit
A: ARNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3875
Polymers24,0111
Non-polymers3764
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.570, 43.570, 71.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein ARNA / ARNA


Mass: 24010.920 Da / Num. of mol.: 1
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: Q4J9H4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.54 Å3/Da / Density % sol: 51.5 % / Description: NONE
Crystal growDetails: RESERVOIR BUFFER: 0.1 M HEPES PH 7.5; 1.5 M LI2SO4 PROTEIN BUFFER: 20 MM TRIS PH 8.0; 100 MM NACL 3.5 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: BESSY / Beamline: 14.1 / Wavelength: 0.91801
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 8, 2012
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91801 Å / Relative weight: 1
ReflectionResolution: 1.75→30.81 Å / Num. obs: 13490 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.18 % / Biso Wilson estimate: 24.82 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 21.95
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 4.24 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.45 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FF4

2ff4


Resolution: 1.75→30.809 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 21.87 / Stereochemistry target values: ML
Details: ONLY RESIDUES P97 - F212 OF ARNA CAN BE SEEN IN THE STRUCTURE, RESIDUES W207 - F212 ARE PART OF THE C-TERMINAL STROP-TAG
RfactorNum. reflection% reflection
Rfree0.1893 685 5.1 %
Rwork0.1675 --
obs0.1686 13488 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.77 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms939 0 22 120 1081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051027
X-RAY DIFFRACTIONf_angle_d1.0021410
X-RAY DIFFRACTIONf_dihedral_angle_d13.118393
X-RAY DIFFRACTIONf_chiral_restr0.06161
X-RAY DIFFRACTIONf_plane_restr0.005177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7502-1.88530.29631360.23712536X-RAY DIFFRACTION99
1.8853-2.0750.22031420.19262547X-RAY DIFFRACTION99
2.075-2.37520.16541420.15762548X-RAY DIFFRACTION100
2.3752-2.99210.19071370.17372563X-RAY DIFFRACTION100
2.9921-30.81340.17751280.15452609X-RAY DIFFRACTION100
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)
16.27131.8226-3.80373.8613-1.51869.4147-0.12980.61510.0972-0.59030.34150.00220.7777-0.4456-0.14520.1808-0.00560.03110.1693-0.00080.14677.04022.4207-9.5167
24.44351.2144-0.98533.7809-1.99566.61790.0238-0.08950.2459-0.02210.0163-0.0293-0.295-0.2149-0.05320.09350.01560.04710.1155-0.04170.12870.944412.4341-4.52
31.7766-0.4235-1.18122.1306-0.46023.30430.27780.1640.3901-0.4037-0.2384-0.9773-0.25450.4143-0.02070.267-0.02290.22990.22060.01520.442114.755817.3925-8.11
42.2843-0.0585-0.59842.051-0.17713.49850.10530.10110.0792-0.0867-0.0541-0.2928-0.2040.4101-0.05430.1041-0.04430.0350.2139-0.03060.145514.12918.5835-2.1582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 97 THROUGH 120 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 121 THROUGH 151 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 152 THROUGH 163 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 164 THROUGH 212 )

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