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- PDB-3ay5: Crystal structure of HHM (human homologue of murine maternal Id-l... -

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Basic information

Entry
Database: PDB / ID: 3ay5
TitleCrystal structure of HHM (human homologue of murine maternal Id-like molecule)
ComponentsCyclin-D1-binding protein 1
KeywordsCELL CYCLE / dominant-negative helix-loop-helix transcriptional regulator
Function / homology
Function and homology information


nuclear body / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Cyclin-D1-binding protein 1 / : / : / Grap2 and cyclin-D-interacting, N-terminal / Grap2 and cyclin-D-interacting, C-terminal / I/LWEQ domain / I/LWEQ domain / Talin, central domain / A middle domain of Talin 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cyclin-D1-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSeto, A. / Ishitani, R. / Nureki, O.
CitationJournal: Embo J. / Year: 2012
Title: Structure of a dominant-negative helix-loop-helix transcriptional regulator suggests mechanisms of autoinhibition.
Authors: Ishii, R. / Isogaya, K. / Seto, A. / Koinuma, D. / Watanabe, Y. / Arisaka, F. / Yaguchi, S. / Ikushima, H. / Dohmae, N. / Miyazono, K. / Miyazawa, K. / Ishitani, R. / Nureki, O.
History
DepositionApr 28, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Cyclin-D1-binding protein 1


Theoretical massNumber of molelcules
Total (without water)40,2701
Polymers40,2701
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.031, 105.031, 124.266
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cyclin-D1-binding protein 1 / Grap2 and cyclin-D-interacting protein / Human homolog of Maid


Mass: 40269.703 Da / Num. of mol.: 1 / Mutation: C198S, C300S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNDBP1, DIP1, GCIP, HHM / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O95273
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 4.91 Å3/Da / Density % sol: 74.97 % / Mosaicity: 0.587 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM imidazole, 500mM (NH4)2HPO4, 100mM NaCl, pH 8.0, 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: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 25654 / % possible obs: 91.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.046 / Χ2: 1.866 / Net I/σ(I): 26
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.543.60.37112631.125191.6
2.54-2.593.70.3712231.144189.7
2.59-2.643.80.36112171.1190
2.64-2.694.20.32212721.229190.7
2.69-2.754.50.30512391.193189.3
2.75-2.824.60.26912061.3189.5
2.82-2.894.90.24912301.358189.6
2.89-2.965.20.20812431.468188.8
2.96-3.055.90.18812651.685191.4
3.05-3.156.40.14112471.759190.5
3.15-3.267.40.1212951.991193.3
3.26-3.398.10.10313762.116196.6
3.39-3.5590.08713302.437196.9
3.55-3.738.50.07613543.112197.3
3.73-3.978.50.05513212.747194.4
3.97-4.278.80.04213262.102193.6
4.27-4.790.03713261.948194.1
4.7-5.389.40.03313631.69195.9
5.38-6.789.90.02914201.448197.9
6.78-508.50.02311381.248174.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30.624 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7853 / SU ML: 0.39 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2612 1271 4.96 %
Rwork0.222 --
obs0.2239 25638 91.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.487 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 205.72 Å2 / Biso mean: 99.6011 Å2 / Biso min: 53.73 Å2
Baniso -1Baniso -2Baniso -3
1-5.5837 Å2-0 Å2-0 Å2
2--5.5837 Å20 Å2
3----11.1675 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 0 52 2385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062367
X-RAY DIFFRACTIONf_angle_d1.0293210
X-RAY DIFFRACTIONf_chiral_restr0.064389
X-RAY DIFFRACTIONf_plane_restr0.005408
X-RAY DIFFRACTIONf_dihedral_angle_d17.797890
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.60020.36551400.35412630277091
2.6002-2.71840.34121280.33142600272890
2.7184-2.86160.37071340.30352629276390
2.8616-3.04080.31551350.27092605274090
3.0408-3.27530.32571420.25012709285192
3.2753-3.60450.28051490.2382849299897
3.6045-4.1250.23261530.19792782293595
4.125-5.19290.19051470.16692832297995
5.1929-30.62630.24761430.20062731287488
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)
17.4878-1.35792.51121.2981-1.1684.5731-0.159-0.86750.06010.40430.0709-0.0507-0.1147-0.3547-0.00140.4841-0.195-0.00771.0903-0.06440.6468-59.211840.910536.9135
24.31962.3081-0.5795.1214-0.28623.87050.03550.06940.06750.0733-0.03230.0967-0.5637-0.2347-0.00130.35310.0959-0.05831.0804-0.10810.5741-24.770349.960823.3383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND RESID 14:167A14 - 167
2X-RAY DIFFRACTION2CHAIN A AND RESID 168:360A168 - 360

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