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- PDB-3omy: Crystal structure of the pED208 TraM N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3omy
TitleCrystal structure of the pED208 TraM N-terminal domain
ComponentsProtein traM
KeywordsDNA BINDING PROTEIN / dimer / bacterial conjugation / ribbon-helix-helix / transcriptional repressor / DNA
Function / homology
Function and homology information


DNA binding / cytoplasm
Similarity search - Function
TraM protein, DNA-binding / Relaxosome protein TraM / TraM, DNA-binding domain / TraM protein, DNA-binding / Integration host factor (IHF)-like DNA-binding domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Relaxosome protein TraM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsWong, J.J.W. / Lu, J. / Edwards, R.A. / Frost, L.S. / Mark Glover, J.N.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structural basis of cooperative DNA recognition by the plasmid conjugation factor, TraM.
Authors: Wong, J.J. / Lu, J. / Edwards, R.A. / Frost, L.S. / Glover, J.N.
History
DepositionAug 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Protein traM
B: Protein traM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1284
Polymers12,0122
Non-polymers1162
Water3,297183
1
A: Protein traM
hetero molecules

A: Protein traM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1964
Polymers12,0122
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3630 Å2
ΔGint-25 kcal/mol
Surface area6130 Å2
MethodPISA
2
B: Protein traM
hetero molecules

B: Protein traM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0604
Polymers12,0122
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3410 Å2
ΔGint-46 kcal/mol
Surface area5890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.069, 54.069, 67.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Protein traM


Mass: 6005.890 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-52
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: traM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33788
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5% PEG 4000, 50mM MES, 5mM magnesium sulphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2008
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 25197 / Num. obs: 25159 / % possible obs: 81 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rsym value: 0.044 / Net I/σ(I): 39.2
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 6.6 / Num. unique all: 2459 / Rsym value: 0.329 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CMB

1cmb


Resolution: 1.3→42.14 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.369 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17293 1284 5.1 %RANDOM
Rwork0.14977 ---
obs0.15092 23875 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.999 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.3→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms805 0 7 183 995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221011
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9851397
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6495144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.43625.88251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25915217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.299156
X-RAY DIFFRACTIONr_chiral_restr0.0890.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02762
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.2011.5591
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9992995
X-RAY DIFFRACTIONr_scbond_it2.973420
X-RAY DIFFRACTIONr_scangle_it4.5954.5381
X-RAY DIFFRACTIONr_rigid_bond_restr1.33231011
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 85 -
Rwork0.222 1721 -
obs--100 %
Refinement TLS params.

T12: 0.0017 Å2 / 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)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8898-0.0302-0.02081.10630.44390.6031-0.04160.06440.02390.0550.04220.01840.0318-0.024-0.00060.0352-0.00010.02410.00030.0766-13.285-5.99936.86
21.0299-0.1510.2840.9087-0.07210.87870.04030.00570.0021-0.0131-0.01020.0644-0.0116-0.0741-0.03020.0276-0.00560.0379-0.00080.08644.3713.45630.525
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 51
2X-RAY DIFFRACTION2B3 - 49

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