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- PDB-5fwh: N-terminal FHA domain from EssC a component of the bacterial Type... -

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Basic information

Entry
Database: PDB / ID: 5fwh
TitleN-terminal FHA domain from EssC a component of the bacterial Type VII secretion apparatus
ComponentsESSC
KeywordsSTRUCTURAL PROTEIN / ATPASE / ESX-1 / FORKHEAD-ASSOCIATED DOMAIN / FTSK/SPOIIIE
Function / homology
Function and homology information


ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane
Similarity search - Function
Firmicutes EssC, N-terminal / Firmicutes EssC, C-terminal / DNA transporter / : / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ESX secretion system protein EccC
Similarity search - Component
Biological speciesGEOBACILLUS THERMODENITRIFICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.06 Å
AuthorsZoltner, M. / Ng, W.M.A.V. / Money, J.J. / Fyfe, P.K. / Kneuper, H. / Palmer, T. / Hunter, W.N.
CitationJournal: Biochem.J. / Year: 2016
Title: Essc: Domain Structures Inform on the Elusive Translocation Channel in the Type Vii Secretion System.
Authors: Zoltner, M. / Ng, W.M.A.V. / Money, J.J. / Fyfe, P.K. / Kneuper, H. / Palmer, T. / Hunter, W.N.
History
DepositionFeb 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESSC


Theoretical massNumber of molelcules
Total (without water)22,2601
Polymers22,2601
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.792, 49.887, 94.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ESSC


Mass: 22260.387 Da / Num. of mol.: 1 / Fragment: FHA DOMAIN, RESIDUES 1-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS THERMODENITRIFICANS (bacteria)
Plasmid: PET27B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4IKE7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES 1-196 ONLY

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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: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.06→29.5 Å / Num. obs: 12092 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 27.3
Reflection shellResolution: 2.06→2.17 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.6 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.06→47.08 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.915 / SU B: 18.873 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31307 574 4.8 %RANDOM
Rwork0.23725 ---
obs0.24097 11479 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.06→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 0 20 1514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191520
X-RAY DIFFRACTIONr_bond_other_d0.0020.021446
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.9642060
X-RAY DIFFRACTIONr_angle_other_deg1.10233323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6515184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.62224.9371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63315253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.124158
X-RAY DIFFRACTIONr_chiral_restr0.1130.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021696
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02342
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_it2.8553.969748
X-RAY DIFFRACTIONr_mcbond_other2.8573.966747
X-RAY DIFFRACTIONr_mcangle_it4.3595.921928
X-RAY DIFFRACTIONr_mcangle_other4.3565.925929
X-RAY DIFFRACTIONr_scbond_it3.1854.399772
X-RAY DIFFRACTIONr_scbond_other3.1834.402773
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6996.4281133
X-RAY DIFFRACTIONr_long_range_B_refined7.07731.3461549
X-RAY DIFFRACTIONr_long_range_B_other7.07731.3291548
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.057→2.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 40 -
Rwork0.323 746 -
obs--90.45 %
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)
19.22840.1687-1.78921.2899-1.88063.0050.37160.147-0.2765-0.1542-0.01320.28650.1842-0.0103-0.35840.19210.03070.0290.0166-0.03260.243234.175-0.63765.455
21.5233-0.6726-0.67010.54881.11496.20050.055-0.0397-0.04570.0598-0.13970.0858-0.2987-0.23910.08470.13-0.09510.02360.1098-0.04180.168532.2274.05568.332
31.6201-1.30661.02081.56250.85026.8644-0.16880.1557-0.00760.1527-0.0020.0738-0.1070.3110.17080.0213-0.0068-0.00260.0820.01920.181141.512-0.68548.08
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION2A22 - 103
3X-RAY DIFFRACTION3A104 - 195

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