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- PDB-2yy0: Crystal Structure of MS0802, c-Myc-1 binding protein domain from ... -

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Basic information

Entry
Database: PDB / ID: 2yy0
TitleCrystal Structure of MS0802, c-Myc-1 binding protein domain from Homo sapiens
ComponentsC-Myc-binding protein
KeywordsTRANSCRIPTION / conserved hypothetical protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


spermatogenesis / transcription coactivator activity / regulation of DNA-templated transcription / mitochondrion / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1060 / Associate of Myc 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
c-Myc-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsXie, Y. / Wang, H. / Ihsanawati, K.T. / Kishishita, S. / Takemoto, C. / Shirozu, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: crystal structure of c-Myc-1 binding protein domain from Homo sapiens
Authors: Xie, Y. / Wang, H. / Ihsanawati, K.T. / Kishishita, S. / Takemoto, C. / Murayama, K. / Shirozu, M. / Yokoyama, S.
History
DepositionApr 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 12, 2024Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / struct_biol / Item: _audit_author.name / _citation_author.name
Revision 1.4Jun 26, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_description / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-Myc-binding protein
B: C-Myc-binding protein
C: C-Myc-binding protein
D: C-Myc-binding protein


Theoretical massNumber of molelcules
Total (without water)24,4724
Polymers24,4724
Non-polymers00
Water81145
1
A: C-Myc-binding protein
B: C-Myc-binding protein


Theoretical massNumber of molelcules
Total (without water)12,2362
Polymers12,2362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-22 kcal/mol
Surface area7260 Å2
MethodPISA
2
C: C-Myc-binding protein
D: C-Myc-binding protein


Theoretical massNumber of molelcules
Total (without water)12,2362
Polymers12,2362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-22.3 kcal/mol
Surface area7360 Å2
MethodPISA
3
A: C-Myc-binding protein
B: C-Myc-binding protein
C: C-Myc-binding protein
D: C-Myc-binding protein

A: C-Myc-binding protein
B: C-Myc-binding protein
C: C-Myc-binding protein
D: C-Myc-binding protein

A: C-Myc-binding protein
B: C-Myc-binding protein
C: C-Myc-binding protein
D: C-Myc-binding protein


Theoretical massNumber of molelcules
Total (without water)73,41612
Polymers73,41612
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area21490 Å2
ΔGint-191.8 kcal/mol
Surface area35190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.634, 59.634, 194.868
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Detailsin this crystal packing, it looks like dimer. But, there is no experimental evidence.

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Components

#1: Protein
C-Myc-binding protein / Associate of Myc 1 / AMY-1


Mass: 6118.013 Da / Num. of mol.: 4 / Fragment: UNP residues 42-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: E.coli extract / Plasmid: PK060110-05-MD01 / Production host: cell free protein synthesis (others) / References: UniProt: Q99417
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M Tris-HCl, 2M NH4H2PO4, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 27, 2006 / Details: Mirror
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 10097 / Num. obs: 10097 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.02 % / Biso Wilson estimate: 30.9 Å2 / Rsym value: 0.07 / Net I/σ(I): 21.63
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 9.83 / Num. unique all: 1444 / Rsym value: 0.265 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→31.11 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1024080.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.289 995 10.3 %RANDOM
Rwork0.244 ---
obs0.244 9646 95.3 %-
all-10097 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.9749 Å2 / ksol: 0.397029 e/Å3
Displacement parametersBiso mean: 58.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.57 Å210.63 Å20 Å2
2--7.57 Å20 Å2
3----15.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.4→31.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1489 0 0 45 1534
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.721.5
X-RAY DIFFRACTIONc_mcangle_it2.912
X-RAY DIFFRACTIONc_scbond_it2.492
X-RAY DIFFRACTIONc_scangle_it3.962.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 152 10.3 %
Rwork0.254 1330 -
obs--88.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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