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- PDB-7ocb: Crystal structure of Spindlin1 in complex with the inhibitor XY49-92B -

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Basic information

Entry
Database: PDB / ID: 7ocb
TitleCrystal structure of Spindlin1 in complex with the inhibitor XY49-92B
ComponentsSpindlin-1
KeywordsCELL CYCLE / chromatin / epigenetics / methyl reader / inhibitor
Function / homology
Function and homology information


gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / Wnt signaling pathway / spindle / chromatin organization / nuclear membrane / regulation of DNA-templated transcription ...gamete generation / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / Wnt signaling pathway / spindle / chromatin organization / nuclear membrane / regulation of DNA-templated transcription / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol
Similarity search - Function
Spindlin/spermiogenesis-specific protein / Spindlin/spermiogenesis-specific domain superfamily / Spin/Ssty Family
Similarity search - Domain/homology
GLYCINE / PHOSPHATE ION / Chem-V88 / Spindlin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsJohansson, C. / Krojer, T. / Park, K. / Xiong, Y. / Jin, J. / Oppermann, U.
CitationJournal: To Be Published
Title: Crystal structure of Spindlin1 in complex with the inhibitor XY49-92B
Authors: Johansson, C. / Krojer, T. / Park, K. / Xiong, Y. / Jin, J. / Oppermann, U.
History
DepositionApr 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Spindlin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5499
Polymers25,5001
Non-polymers1,0508
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-56 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.477, 115.477, 43.721
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules B

#1: Protein Spindlin-1 / Ovarian cancer-related protein / Spindlin1


Mass: 25499.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN1, OCR, SPIN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y657

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Non-polymers , 7 types, 181 molecules

#2: Chemical ChemComp-V88 / 7-[3-(1,3-dihydroisoindol-2-yl)propoxy]-2N-[2-(dimethylamino)ethyl]-6-methoxy-4N-(1-propan-2-ylpiperidin-4-yl)quinazoline-2,4-diamine


Mass: 561.761 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H47N7O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 55-60 % MPD and 0.1 M SPG buffer pH 5.5-6.0 / PH range: 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.42→81.67 Å / Num. obs: 56337 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 14.87 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.032 / Rrim(I) all: 0.11 / Net I/σ(I): 10.8 / Num. measured all: 603240 / Scaling rejects: 388
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.42-1.466.81.27240930.6730.5221.377
81.66-81.6610.80.0637460.9250.0210.066

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.45 Å81.65 Å
Translation5.45 Å81.65 Å

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Processing

Software
NameVersionClassification
PHENIX1.12-2829refinement
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.0phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I8L

6i8l


Resolution: 1.42→81.655 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 2806 4.99 %
Rwork0.1801 53437 -
obs0.1814 56243 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.86 Å2 / Biso mean: 22.1735 Å2 / Biso min: 7.91 Å2
Refinement stepCycle: final / Resolution: 1.42→81.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 0 145 173 1877
Biso mean--26.58 31.16 -
Num. residues----196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121703
X-RAY DIFFRACTIONf_angle_d1.1972317
X-RAY DIFFRACTIONf_chiral_restr0.1246
X-RAY DIFFRACTIONf_plane_restr0.009316
X-RAY DIFFRACTIONf_dihedral_angle_d20.917637
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.42-1.44410.2991320.299261299
1.4441-1.47040.33271490.28392609100
1.4704-1.49870.32581480.26242625100
1.4987-1.52930.23821380.23822613100
1.5293-1.56250.21761440.21222659100
1.5625-1.59890.22171360.20032613100
1.5989-1.63890.25271470.19642629100
1.6389-1.68320.18291370.18292673100
1.6832-1.73270.1991310.18052635100
1.7327-1.78870.20571170.17412667100
1.7887-1.85260.20041440.16862641100
1.8526-1.92680.15931380.15932673100
1.9268-2.01450.19561410.15612656100
2.0145-2.12070.16341420.15512664100
2.1207-2.25360.16161350.15492692100
2.2536-2.42760.17561390.16552700100
2.4276-2.67190.20011340.16942691100
2.6719-3.05850.20371580.17142707100
3.0585-3.85340.22471410.17092774100
3.8534-81.6550.21411550.19072904100
Refinement TLS params.Method: refined / Origin x: -8.057 Å / Origin y: -33.889 Å / Origin z: 6.443 Å
111213212223313233
T0.0722 Å20.0185 Å2-0.005 Å2-0.087 Å2-0.0066 Å2--0.0984 Å2
L0.6292 °2-0.3869 °2-0.0583 °2-1.2765 °2-0.1239 °2--1.3106 °2
S0.0289 Å °0.0397 Å °0.0458 Å °-0.0498 Å °-0.0317 Å °-0.0442 Å °-0.116 Å °-0.0664 Å °0.0045 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND ( RESID 301:301 OR RESID 303:304 OR RESID 52:269 OR RESID 302:302 OR RESID 306:306 OR RESID 305:305 OR RESID 307:308 OR RESID 401:573 ) )B301
2X-RAY DIFFRACTION1( CHAIN B AND ( RESID 301:301 OR RESID 303:304 OR RESID 52:269 OR RESID 302:302 OR RESID 306:306 OR RESID 305:305 OR RESID 307:308 OR RESID 401:573 ) )B303 - 304
3X-RAY DIFFRACTION1( CHAIN B AND ( RESID 301:301 OR RESID 303:304 OR RESID 52:269 OR RESID 302:302 OR RESID 306:306 OR RESID 305:305 OR RESID 307:308 OR RESID 401:573 ) )B52 - 269
4X-RAY DIFFRACTION1( CHAIN B AND ( RESID 301:301 OR RESID 303:304 OR RESID 52:269 OR RESID 302:302 OR RESID 306:306 OR RESID 305:305 OR RESID 307:308 OR RESID 401:573 ) )B302
5X-RAY DIFFRACTION1( CHAIN B AND ( RESID 301:301 OR RESID 303:304 OR RESID 52:269 OR RESID 302:302 OR RESID 306:306 OR RESID 305:305 OR RESID 307:308 OR RESID 401:573 ) )B306
6X-RAY DIFFRACTION1( CHAIN B AND ( RESID 301:301 OR RESID 303:304 OR RESID 52:269 OR RESID 302:302 OR RESID 306:306 OR RESID 305:305 OR RESID 307:308 OR RESID 401:573 ) )B305
7X-RAY DIFFRACTION1( CHAIN B AND ( RESID 301:301 OR RESID 303:304 OR RESID 52:269 OR RESID 302:302 OR RESID 306:306 OR RESID 305:305 OR RESID 307:308 OR RESID 401:573 ) )B307 - 308
8X-RAY DIFFRACTION1( CHAIN B AND ( RESID 301:301 OR RESID 303:304 OR RESID 52:269 OR RESID 302:302 OR RESID 306:306 OR RESID 305:305 OR RESID 307:308 OR RESID 401:573 ) )B401 - 573

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