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- PDB-1q87: Crystal structure of the C-domain of the T.vaginalis Inr binding ... -

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Basic information

Entry
Database: PDB / ID: 1q87
TitleCrystal structure of the C-domain of the T.vaginalis Inr binding protein, IBP39 (tetragonal form)
Components39 kDa initiator binding protein
KeywordsDNA BINDING PROTEIN / Initiator / Inr / Initiator binding protein / core promoter
Function / homologyInitiator binding domain / Initiator binding protein 39kDa, C-terminal / IBP39, C-terminal domain superfamily / Transcription-initiator DNA-binding domain IBD / Initiator binding protein 39 kDa / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / metal ion binding / 39 kDa initiator binding protein
Function and homology information
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsSchumacher, M.A. / Johnson, P.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Structural Basis of Core Promoter Recognition in a Primitive Eukaryote
Authors: Schumacher, M.A. / Lau, A.O.T. / Johnson, P.J.
History
DepositionAug 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 39 kDa initiator binding protein
B: 39 kDa initiator binding protein


Theoretical massNumber of molelcules
Total (without water)51,4542
Polymers51,4542
Non-polymers00
Water1,09961
1
A: 39 kDa initiator binding protein


Theoretical massNumber of molelcules
Total (without water)25,7271
Polymers25,7271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 39 kDa initiator binding protein


Theoretical massNumber of molelcules
Total (without water)25,7271
Polymers25,7271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.420, 76.420, 157.620
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 39 kDa initiator binding protein


Mass: 25727.221 Da / Num. of mol.: 2 / Fragment: C-domain, residues 127-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: ibp39 / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95VR4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.23 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 5000, ammonium sulphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120-50 mg/mlprotein1drop
2200 mMammonium sulfate1reservoir
350 mMMES1reservoirpH6.5
425 %PEG50001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 12, 2002
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.32→65 Å / Num. obs: 19164 / % possible obs: 91.6 % / Observed criterion σ(F): 11 / Observed criterion σ(I): 10.9 / Redundancy: 5.8 % / Biso Wilson estimate: 57.5 Å2 / Rmerge(I) obs: 0.042
Reflection shellResolution: 2.32→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2 / % possible all: 91.6
Reflection
*PLUS
Lowest resolution: 65 Å / Num. measured all: 111463

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q88, C-domain from the C2 monoclinic form

1q88


Resolution: 2.32→65 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1778869.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1891 9.9 %RANDOM
Rwork0.215 ---
all0.22 ---
obs0.215 19111 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.8645 Å2 / ksol: 0.351692 e/Å3
Displacement parametersBiso mean: 66.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.32 Å20 Å20 Å2
2---5.32 Å20 Å2
3---10.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.32→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3054 0 0 61 3115
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d1.05
LS refinement shellResolution: 2.32→2.47 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 238 10.5 %
Rwork0.309 2038 -
obs--66.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.275
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05

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