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- PDB-2db7: Crystal structure of hypothetical protein MS0332 -

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Basic information

Entry
Database: PDB / ID: 2db7
TitleCrystal structure of hypothetical protein MS0332
ComponentsHairy/enhancer-of-split related with YRPW motif 1
KeywordsTRANSCRIPTION / STRUCTURAL GENOMICS / UNKNOWN FUNCTION / DNA BINDING PROTEIN / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


umbilical cord morphogenesis / regulation of vasculogenesis / atrioventricular valve formation / dorsal aorta morphogenesis / arterial endothelial cell differentiation / negative regulation of smooth muscle cell differentiation / cardiac ventricle morphogenesis / circulatory system development / cardiac epithelial to mesenchymal transition / cardiac conduction system development ...umbilical cord morphogenesis / regulation of vasculogenesis / atrioventricular valve formation / dorsal aorta morphogenesis / arterial endothelial cell differentiation / negative regulation of smooth muscle cell differentiation / cardiac ventricle morphogenesis / circulatory system development / cardiac epithelial to mesenchymal transition / cardiac conduction system development / pulmonary valve morphogenesis / negative regulation of biomineral tissue development / heart trabecula formation / aortic valve morphogenesis / Cardiogenesis / NOTCH4 Intracellular Domain Regulates Transcription / anterior/posterior pattern specification / labyrinthine layer blood vessel development / NOTCH3 Intracellular Domain Regulates Transcription / endocardial cushion morphogenesis / ventricular septum morphogenesis / negative regulation of Notch signaling pathway / cardiac septum morphogenesis / RUNX2 regulates osteoblast differentiation / regulation of neurogenesis / negative regulation of neuron differentiation / cis-regulatory region sequence-specific DNA binding / Notch signaling pathway / NOTCH1 Intracellular Domain Regulates Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / sequence-specific double-stranded DNA binding / angiogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #980 / Orange domain / : / Hairy Orange / Orange domain profile. / Orange domain / Helix-loop-helix DNA-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #980 / Orange domain / : / Hairy Orange / Orange domain profile. / Orange domain / Helix-loop-helix DNA-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Helix non-globular / Special
Similarity search - Domain/homology
Hairy/enhancer-of-split related with YRPW motif protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsWang, H. / Takemoto-Hori, C. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of hypothetical protein MS0332
Authors: Wang, H. / Takemoto-Hori, C. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionDec 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hairy/enhancer-of-split related with YRPW motif 1
B: Hairy/enhancer-of-split related with YRPW motif 1


Theoretical massNumber of molelcules
Total (without water)14,0392
Polymers14,0392
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-22 kcal/mol
Surface area7140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.322, 44.810, 92.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hairy/enhancer-of-split related with YRPW motif 1 / MS0332 / Hairy and enhancer of split related-1 / HESR-1 / Cardiovascular helix-loop-helix factor 2 ...MS0332 / Hairy and enhancer of split related-1 / HESR-1 / Cardiovascular helix-loop-helix factor 2 / HES-related repressor protein 2 HERP2


Mass: 7019.605 Da / Num. of mol.: 2 / Fragment: Hairy protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Plasmid: PX041202-21 / References: UniProt: Q9Y5J3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: PEG3350, Magnesium Chloride, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9789, 0.9791, 0.9650
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 18, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97911
30.9651
ReflectionResolution: 1.9→50 Å / Num. obs: 9565 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 11.7 Å2 / Rsym value: 0.082 / Net I/σ(I): 19.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 10.1 / Num. unique all: 931 / Rsym value: 0.151 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→27.07 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 586480.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.22 503 5.3 %RANDOM
Rwork0.192 ---
obs0.192 9446 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.2791 Å2 / ksol: 0.389036 e/Å3
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å20 Å20 Å2
2--4.38 Å20 Å2
3----2.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms898 0 0 97 995
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d16.6
X-RAY DIFFRACTIONc_improper_angle_d0.59
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.23 89 5.8 %
Rwork0.2 1457 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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