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- PDB-1pp8: crystal structure of the T. vaginalis IBP39 Initiator binding dom... -

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Basic information

Entry
Database: PDB / ID: 1pp8
Titlecrystal structure of the T. vaginalis IBP39 Initiator binding domain (IBD) bound to the alpha-SCS Inr element
Components
  • (ALPHA-SCS INR) x 2
  • 39 kDa initiator binding protein
KeywordsTranscription/DNA / IBP39 / Initiator binding protein / Inr / core promoter / transcription / T. vaginalis / Transcription-DNA COMPLEX
Function / homology
Function and homology information


Initiator 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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / 39 kDa initiator binding protein
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.05 Å
AuthorsSchumacher, M.A. / Lau, A.O.T. / 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
DepositionJun 16, 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 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _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

Downloads & links

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Assembly

Deposited unit
E: ALPHA-SCS INR
I: ALPHA-SCS INR
Y: ALPHA-SCS INR
K: ALPHA-SCS INR
T: ALPHA-SCS INR
R: ALPHA-SCS INR
J: ALPHA-SCS INR
G: ALPHA-SCS INR
U: 39 kDa initiator binding protein
P: 39 kDa initiator binding protein
F: 39 kDa initiator binding protein
V: 39 kDa initiator binding protein
M: 39 kDa initiator binding protein
O: 39 kDa initiator binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,55416
Polymers121,36214
Non-polymers1922
Water0
1
K: ALPHA-SCS INR
J: ALPHA-SCS INR
F: 39 kDa initiator binding protein


Theoretical massNumber of molelcules
Total (without water)22,6683
Polymers22,6683
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Y: ALPHA-SCS INR
R: ALPHA-SCS INR
M: 39 kDa initiator binding protein


Theoretical massNumber of molelcules
Total (without water)22,6683
Polymers22,6683
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: ALPHA-SCS INR
G: ALPHA-SCS INR
U: 39 kDa initiator binding protein


Theoretical massNumber of molelcules
Total (without water)22,6683
Polymers22,6683
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: ALPHA-SCS INR
T: ALPHA-SCS INR
P: 39 kDa initiator binding protein


Theoretical massNumber of molelcules
Total (without water)22,6683
Polymers22,6683
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
V: 39 kDa initiator binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4402
Polymers15,3441
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
O: 39 kDa initiator binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4402
Polymers15,3441
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)292.000, 292.000, 292.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Detailsthe crystallographic asymmetric unit contains two apo IBDs and four IBD-alphaSCS complexes that are arranged as a pseudocontinous helix. Because extra IBD was used in the crystallization, there are extra apo IBDs.

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Components

#1: DNA chain
ALPHA-SCS INR


Mass: 3597.367 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: the alpha-SCS Inr promoter element, DNA site
#2: DNA chain
ALPHA-SCS INR


Mass: 3726.453 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Protein
39 kDa initiator binding protein


Mass: 15344.390 Da / Num. of mol.: 6 / Fragment: residues 1-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: Trichomonas vaginalis:IBP39 / Plasmid: pEQ60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95VR4
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 4.23 Å3/Da / Density % sol: 70.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Ammonium sulphate, MES pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium sulphate11
2MES11
3H2O11
4Ammonium sulphate12
Crystal grow
*PLUS
Temperature: 298 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
22.5 Mammonium sulfate1reservoir
30.1 MMES1reservoirpH5.6
41

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 3, 2002
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 3.05→146 Å / Num. all: 38349 / Num. obs: 36349 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 99.9 Å2 / Rsym value: 0.064 / Net I/σ(I): 7.3
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.488 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.05→146 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: after structure determination, minimal refinement was carried out in CNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.311 1836 5 %RANDOM
Rwork0.269 ---
all0.272 38349 --
obs0.269 36045 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 190.751 Å2 / ksol: 0.327975 e/Å3
Displacement parametersBiso mean: 99.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 3.05→146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5314 1944 10 0 7268
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d1.63
X-RAY DIFFRACTIONc_mcbond_it3.631.5
X-RAY DIFFRACTIONc_mcangle_it6.182
X-RAY DIFFRACTIONc_scbond_it6.222
X-RAY DIFFRACTIONc_scangle_it9.822.5
LS refinement shellResolution: 3.05→3.24 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 247 5.2 %
Rwork0.384 4489 -
obs--73.3 %
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.63

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