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- PDB-1e9r: Bacterial conjugative coupling protein TrwBdeltaN70. Trigonal for... -

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Basic information

Entry
Database: PDB / ID: 1e9r
TitleBacterial conjugative coupling protein TrwBdeltaN70. Trigonal form in complex with sulphate.
ComponentsCONJUGAL TRANSFER PROTEIN TRWB
KeywordsCOUPLING PROTEIN / BACTERIAL CONJUGATION / F1-ATPASE-LIKE QUATERNARY STRUCTURE / RING HELICASES
Function / homology
Function and homology information


nucleotide binding / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Type IV secretion system coupling protein TraD, DNA-binding domain / Type IV secretion-system coupling protein DNA-binding domain / Magnesium chelatase subunit I, C-Terminal domain / : / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Type IV secretion system coupling protein TraD, DNA-binding domain / Type IV secretion-system coupling protein DNA-binding domain / Magnesium chelatase subunit I, C-Terminal domain / : / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsGomis-Rueth, F.X. / Moncalian, G. / Cabezon, E. / de la Cruz, F. / Coll, M.
CitationJournal: Nature / Year: 2001
Title: The Bacterial Conjugation Protein Trwb Resembles Ring Helicases and F1-ATPase
Authors: Gomis-Rueth, F.X. / Moncalian, G. / Perez-Luque, R. / Gonzalez, A. / Cabezon, E. / De La Cruz, F. / Coll, M.
History
DepositionOct 26, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: CONJUGAL TRANSFER PROTEIN TRWB
B: CONJUGAL TRANSFER PROTEIN TRWB
D: CONJUGAL TRANSFER PROTEIN TRWB
E: CONJUGAL TRANSFER PROTEIN TRWB
F: CONJUGAL TRANSFER PROTEIN TRWB
G: CONJUGAL TRANSFER PROTEIN TRWB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,47021
Polymers292,0296
Non-polymers1,44115
Water17,330962
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)151.300, 151.300, 258.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein
CONJUGAL TRANSFER PROTEIN TRWB


Mass: 48671.469 Da / Num. of mol.: 6 / Fragment: TRANSMEMBRANE-ANCHOR-EXCISED PROTEIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Gene: TRWB / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q04230
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 962 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B, D, E, F, G FIRST 70 RESIDUES DELETED

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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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growpH: 7.5
Details: 1.5 M AMMONIUM SULPHATE, 0.1 M NACL, 0.1 M HEPES PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.5 Mammonium sulfate1drop
20.1 M1dropNaCl
30.1 MHEPES1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.844
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.844 Å / Relative weight: 1
ReflectionResolution: 2.4→72.6 Å / Num. obs: 1205165 / % possible obs: 100 % / Redundancy: 9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 9

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
SHELXphasing
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 -7 %RANDOM
Rwork0.21 ---
obs0.21 133904 99.9 %-
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19681 0 75 962 20718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.393
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 43 Å2

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