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- PDB-2g9e: Protonation-mediated structural flexibility in the F conjugation ... -

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Basic information

Entry
Database: PDB / ID: 2g9e
TitleProtonation-mediated structural flexibility in the F conjugation regulatory protein, TRAM
ComponentsProtein traM
KeywordsDNA BINDING PROTEIN / FOUR HELIX BUNDLE / TETRAMER / E88L MUTANT
Function / homology
Function and homology information


DNA binding / cytoplasm
Similarity search - Function
Helix Hairpins - #2320 / Relaxosome protein TraM / TraM, DNA-binding domain / TraM protein, DNA-binding / Integration host factor (IHF)-like DNA-binding domain superfamily / Helix Hairpins / 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: 1.8 Å
AuthorsLu, J. / Edwards, R.A. / Wong, J.J. / Manchak, J. / Scott, P.G. / Frost, L.S. / Glover, J.N.
CitationJournal: Embo J. / Year: 2006
Title: Protonation-mediated structural flexibility in the F conjugation regulatory protein, TraM.
Authors: Lu, J. / Edwards, R.A. / Wong, J.J. / Manchak, J. / Scott, P.G. / Frost, L.S. / Glover, J.N.
History
DepositionMar 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein traM


Theoretical massNumber of molelcules
Total (without water)7,9651
Polymers7,9651
Non-polymers00
Water75742
1
A: Protein traM

A: Protein traM

A: Protein traM

A: Protein traM


Theoretical massNumber of molelcules
Total (without water)31,8604
Polymers31,8604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area10960 Å2
ΔGint-137 kcal/mol
Surface area14190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.939, 50.939, 46.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
DetailsBiological tetramer is formed around a four-fold crystallographic axis. REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z

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Components

#1: Protein Protein traM


Mass: 7964.942 Da / Num. of mol.: 1 / Mutation: E88L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: traM / Plasmid: PT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P10026
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.9 Å3/Da / Density % sol: 35.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 400, 0.1M MES PH 6.5, 2MM DTT, 0.5M AMMONIUM ACETATE , pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2005
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.8→36.01 Å / Num. all: 5552 / Num. obs: 5552 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.045 / Rsym value: 0.047 / Net I/σ(I): 25.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.38 / Num. unique all: 232 / Rsym value: 0.363 / % possible all: 84.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G7O

2g7o


Resolution: 1.8→36.01 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.902 / SU B: 6.197 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24459 262 4.7 %RANDOM
Rwork0.18231 ---
all0.18511 5288 --
obs0.18511 5288 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.832 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---0.5 Å20 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms543 0 0 42 585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.97740
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.777567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93125.92627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08715106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.767152
X-RAY DIFFRACTIONr_chiral_restr0.0830.283
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02411
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.2227
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.2400
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5651.5348
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0232551
X-RAY DIFFRACTIONr_scbond_it1.8423220
X-RAY DIFFRACTIONr_scangle_it2.9784.5189
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 10 -
Rwork0.284 354 -
obs--89 %
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)
12.0150.43723.67930.8621.133413.39060.1119-0.05010.01680.00540.1297-0.0318-0.3199-0.0847-0.2416-0.19520.00810.0501-0.21010.0218-0.0827-1.3435.861-19.788
20.29650.351-1.57112.6333-3.308316.22710.12290.20570.26880.1630.30950.28910.3285-1.2902-0.4324-0.1311-0.0907-0.02460.02740.11860.025-15.583-6.822-18.136
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA60 - 913 - 34
2X-RAY DIFFRACTION2AA101 - 12744 - 70

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