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- PDB-1e9s: Bacterial conjugative coupling protein TrwBdeltaN70. Unbound mono... -

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Basic information

Entry
Database: PDB / ID: 1e9s
TitleBacterial conjugative coupling protein TrwBdeltaN70. Unbound monoclinic form.
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
H: CONJUGAL TRANSFER PROTEIN TRWB
I: CONJUGAL TRANSFER PROTEIN TRWB
J: CONJUGAL TRANSFER PROTEIN TRWB
K: CONJUGAL TRANSFER PROTEIN TRWB
L: CONJUGAL TRANSFER PROTEIN TRWB
M: CONJUGAL TRANSFER PROTEIN TRWB


Theoretical massNumber of molelcules
Total (without water)584,05812
Polymers584,05812
Non-polymers00
Water27,8511546
1
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


Theoretical massNumber of molelcules
Total (without water)292,0296
Polymers292,0296
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
H: CONJUGAL TRANSFER PROTEIN TRWB
I: CONJUGAL TRANSFER PROTEIN TRWB
J: CONJUGAL TRANSFER PROTEIN TRWB
K: CONJUGAL TRANSFER PROTEIN TRWB
L: CONJUGAL TRANSFER PROTEIN TRWB
M: CONJUGAL TRANSFER PROTEIN TRWB


Theoretical massNumber of molelcules
Total (without water)292,0296
Polymers292,0296
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)107.400, 153.400, 162.500
Angle α, β, γ (deg.)90.00, 94.20, 90.00
Int Tables number4
Space group name H-MP1211
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.: 12 / Fragment: TRANSMEMBRANE-ANCHOR-EXCISED PROTEIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: TWO HOMOHEXAMERS ARE PRESENT IN THE A.U. / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Gene: TRWB / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q04230
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1546 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B, D, E, F, G, H, I, J, K, L, M 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: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growpH: 7.5 / Details: 0.9 M POTASSIUM/SODIUM, 0.1 M HEPES PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.9 Mpotassium/sodium tartrate1drop
20.1 MHEPES1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.053
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.053 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 728622 / % possible obs: 97 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 9.9

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
SHELXphasing
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRIGONAL CRYSTAL FORM

Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 -7 %RANDOM
Rwork0.209 ---
obs0.209 176179 97.2 %-
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39967 0 0 1546 41513
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_deg1.387
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
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.8 Å2

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