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- PDB-3wz3: Structure of a periplasmic fragment of TraM -

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Basic information

Entry
Database: PDB / ID: 3wz3
TitleStructure of a periplasmic fragment of TraM
ComponentsTraM protein
KeywordsUNKNOWN FUNCTION / type IVB secretion
Function / homologyType-IV b secretion system, inner-membrane complex component / Type-IV b secretion system, inner-membrane complex component / TraM protein
Function and homology information
Biological speciesPlasmid R64 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsKuroda, T. / Kubori, T. / Uchida, Y. / Nagai, H. / Imada, K.
CitationJournal: Sci Rep / Year: 2015
Title: Molecular and structural analysis of Legionella DotI gives insights into an inner membrane complex essential for type IV secretion
Authors: Kuroda, T. / Kubori, T. / Thanh Bui, X. / Hyakutake, A. / Uchida, Y. / Imada, K. / Nagai, H.
History
DepositionSep 18, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: TraM protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5402
Polymers16,4431
Non-polymers961
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.757, 67.757, 73.623
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-555-

HOH

21A-595-

HOH

31A-618-

HOH

DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein TraM protein


Mass: 16443.484 Da / Num. of mol.: 1 / Fragment: periplasmic fragment, UNP residues 91-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmid R64 (others) / Gene: traM / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9R2H2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.05M Glycine pH9.0, 0.8M Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 16, 2011
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.5→24.9 Å / Num. all: 27756 / Num. obs: 27756 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.1 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 17.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 21.4 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 8.9 / Num. unique all: 3907 / % possible all: 98

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Processing

Software
NameVersionClassification
SPring-8BBSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→23.956 Å / SU ML: 0.26 / σ(F): 1.43 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 2008 7.24 %RANDOM
Rwork0.1804 ---
obs0.1823 27723 98.78 %-
all-27723 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.469 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0231 Å20 Å2-0 Å2
2---1.0231 Å20 Å2
3---2.0462 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 5 230 1320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091135
X-RAY DIFFRACTIONf_angle_d1.2191538
X-RAY DIFFRACTIONf_dihedral_angle_d14.596425
X-RAY DIFFRACTIONf_chiral_restr0.09166
X-RAY DIFFRACTIONf_plane_restr0.005199
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5001-1.53760.21491440.1803176597
1.5376-1.57920.21091400.1765178098
1.5792-1.62560.19921360.1749179598
1.6256-1.67810.21430.1738178398
1.6781-1.7380.20741360.172181699
1.738-1.80760.20531430.1724179098
1.8076-1.88980.20971360.1753183799
1.8898-1.98940.21491410.1728181099
1.9894-2.1140.25031430.1759184199
2.114-2.27710.20191430.1727184899
2.2771-2.5060.18321350.1809185599
2.506-2.86820.20911470.1861879100
2.8682-3.61160.19311580.18721897100
3.6116-23.95870.21241630.18742019100

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