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- PDB-4kcx: BRDT in complex with Dinaciclib -

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Basic information

Entry
Database: PDB / ID: 4kcx
TitleBRDT in complex with Dinaciclib
ComponentsBromodomain testis-specific protein
KeywordsCell Cycle/Inhibitor / BRDT / BROMODOMAIN CONTAINING PROTEIN TESTIS SPECIFIC / Cell Cycle-Inhibitor complex
Function / homology
Function and homology information


sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / RNA splicing / histone reader activity / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity ...sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / RNA splicing / histone reader activity / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity / chromatin remodeling / regulation of DNA-templated transcription / positive regulation of gene expression / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1QK / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMartin, M.P. / Schonbrunn, E.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Cyclin-dependent kinase inhibitor dinaciclib interacts with the acetyl-lysine recognition site of bromodomains.
Authors: Martin, M.P. / Olesen, S.H. / Georg, G.I. / Schonbrunn, E.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Bromodomain testis-specific protein
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7275
Polymers27,8962
Non-polymers8303
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-24 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.720, 29.950, 71.380
Angle α, β, γ (deg.)90.00, 94.12, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChain A and B form homodimer

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Components

#1: Protein Bromodomain testis-specific protein / Cancer/testis antigen 9 / CT9 / RING3-like protein


Mass: 13948.153 Da / Num. of mol.: 2 / Fragment: First Bromodomain, UNP residues 21-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRDT / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q58F21
#2: Chemical ChemComp-1QK / 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium / DINACICLIB


Mass: 397.494 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25mM HEPES PH 7.5, 0.1M NaCl, 1mM DTT 0.1M KSCN, 7% PEG3350, 5% ETGLY, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 18535 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 7.7
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2488 / Rsym value: 0.624 / % possible all: 98.1

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FLP

4flp


Resolution: 2→19.811 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 30.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.253 927 5 %RANDOM
Rwork0.2092 ---
obs0.2114 18535 97.91 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.556 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.6694 Å2-0 Å2-0.368 Å2
2---12.236 Å2-0 Å2
3----3.4334 Å2
Refinement stepCycle: LAST / Resolution: 2→19.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 59 137 1970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081889
X-RAY DIFFRACTIONf_angle_d1.1892555
X-RAY DIFFRACTIONf_dihedral_angle_d19.019741
X-RAY DIFFRACTIONf_chiral_restr0.088267
X-RAY DIFFRACTIONf_plane_restr0.005314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10530.36731300.3142478X-RAY DIFFRACTION98
2.1053-2.23710.28531320.25782500X-RAY DIFFRACTION99
2.2371-2.40950.30351330.23012523X-RAY DIFFRACTION99
2.4095-2.65150.28591330.2232533X-RAY DIFFRACTION99
2.6515-3.0340.27351330.2152525X-RAY DIFFRACTION98
3.034-3.8180.23851310.18342494X-RAY DIFFRACTION96
3.818-19.81230.20421350.18012555X-RAY DIFFRACTION96
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)
14.82594.0396-1.49114.4417-2.13933.6872-0.12060.10720.4528-0.360.14871.6767-0.2868-0.7237-0.01770.39320.0278-0.12480.243-0.06860.670511.7026-24.98872.5745
23.3581-2.8513-0.87995.15221.1510.85880.01620.22740.1419-0.2603-0.1211-0.0377-0.1394-0.05610.02390.5618-0.0016-0.05360.10430.02180.137332.8827-28.99070.627
36.1663-0.5343-0.75442.5572-0.21593.05060.1232-0.143-0.3879-0.02560.00640.16330.1772-0.0393-0.05660.06180.0752-0.13010.14710.00650.194428.9362-36.25236.8546
43.63091.96650.92481.50841.52622.6103-0.44490.5812-0.4842-1.02520.3010.80180.4821-0.53710.12310.52-0.0472-0.19350.2765-0.03880.553212.9135-36.2043-0.5664
58.31342.6053.58715.74931.44094.00290.05650.0022-0.0545-0.3932-0.25450.77970.1292-0.35220.23660.3824-0.0149-0.00880.1537-0.05710.149719.5772-32.68610.7093
61.1435-1.1584-2.28611.17352.31554.5689-0.0304-0.20290.16350.04160.3931-0.2491-0.24821.0442-0.3660.5987-0.0467-0.03520.2698-0.0440.132532.0026-22.933415.6904
74.44082.2966-1.564.7644-0.95793.99630.38340.18650.61550.0765-0.13821.273-0.5758-0.5057-0.16350.48510.1353-0.04570.2065-0.03610.450714.8342-22.855811.893
86.4968-5.50173.10565.4221-2.76832.7866-0.0332-0.3479-0.56120.6220.05641.49820.128-0.4786-0.20630.7538-0.02350.13330.2497-0.06470.54869.6736-34.124430.1931
95.4922-0.53091.25563.57970.2631.7107-0.024-0.17360.08630.2735-0.04110.4106-0.1485-0.19280.0650.5975-0.0130.11060.1166-0.02990.138521.4265-25.155932.538
102.3498-1.9568-1.45863.04980.03022.52750.0182-0.02170.19110.3784-0.11920.5429-0.0987-0.30910.10070.55820.00880.0570.2158-0.06180.265618.5994-26.419923.1814
110.42060.14721.47830.05150.51715.19350.0061-0.011-0.0381-0.1265-0.1751-0.07320.01930.88720.16580.76480.03360.01520.23210.00670.162731.7218-36.1220.072
124.0737-5.03013.15147.5-2.16974.73290.3314-0.1894-1.0029-0.044-0.10011.20940.4587-0.4475-0.27410.5471-0.09390.01440.1734-0.05450.31213.93-36.36521.2449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 29:52)
2X-RAY DIFFRACTION2chain 'A' and (resseq 53:65)
3X-RAY DIFFRACTION3chain 'A' and (resseq 66:75)
4X-RAY DIFFRACTION4chain 'A' and (resseq 76:90)
5X-RAY DIFFRACTION5chain 'A' and (resseq 91:108)
6X-RAY DIFFRACTION6chain 'A' and (resseq 109:113)
7X-RAY DIFFRACTION7chain 'A' and (resseq 114:134)
8X-RAY DIFFRACTION8chain 'B' and (resseq 29:52)
9X-RAY DIFFRACTION9chain 'B' and (resseq 53:90)
10X-RAY DIFFRACTION10chain 'B' and (resseq 91:108)
11X-RAY DIFFRACTION11chain 'B' and (resseq 109:113)
12X-RAY DIFFRACTION12chain 'B' and (resseq 114:134)

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