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- PDB-9ejo: Crystal structure of WDR91 in complex with XS381295 -

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Basic information

Entry
Database: PDB / ID: 9ejo
TitleCrystal structure of WDR91 in complex with XS381295
ComponentsWD repeat-containing protein 91
KeywordsTRANSPORT PROTEIN / WD-repeat / WDR / WDR91 / protein transport / ligand / SGC
Function / homology
Function and homology information


phosphatidylinositol 3-kinase inhibitor activity / early endosome to late endosome transport / phosphatidylinositol 3-kinase regulator activity / regulation of protein catabolic process / CDC42 GTPase cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / late endosome membrane / early endosome membrane / endosome membrane / cytosol
Similarity search - Function
WD repeat-containing protein 91 / : / Armc9, CTLH-like domain / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / WD repeat-containing protein 91
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZeng, H. / Ahmad, H. / Wang, X. / Sun, J. / Dong, A. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Peng, H. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Crystal structure of WDR91 in complex with XS381295
Authors: Zeng, H. / Ahmad, H. / Wang, X. / Sun, J. / Dong, A. / Seitova, A. / Arrowsmith, C.H. / Edwards, A.M. / Peng, H. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionNov 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein 91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4853
Polymers41,0641
Non-polymers4212
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.632, 132.382, 119.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein WD repeat-containing protein 91 / WDR91


Mass: 41064.477 Da / Num. of mol.: 1 / Fragment: UNP residues 392-747
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR91, HSPC049 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A4D1P6
#2: Chemical ChemComp-A1BIV / 6-(4-chlorophenyl)-1-methyl-5-[(3S)-1-methyl-2-oxo-2,3-dihydro-1H-indol-3-yl]-1H-pyrrolo[2,3-d]pyrimidine-2,4(3H,7H)-dione


Mass: 420.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H17ClN4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.79 Å3/Da / Density % sol: 67.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.03M of each divalent cation, 0.1M MES/imidazole pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 24659 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.039 / Rrim(I) all: 0.095 / Χ2: 1.021 / Net I/σ(I): 9.7 / Num. measured all: 146990
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.4-2.4460.96612070.7160.9130.431.0590.95100
2.44-2.4960.88212180.7460.9240.3940.9680.968100
2.49-2.5360.70712100.790.940.3130.7740.984100
2.53-2.5960.60712210.8430.9560.2710.6660.967100
2.59-2.6460.56112250.8880.970.2490.6141.03100
2.64-2.760.45712180.8880.970.2030.5011.184100
2.7-2.7760.36711960.9410.9850.1630.4030.991100
2.77-2.8560.3112490.9590.9890.1380.341.018100
2.85-2.936.10.27112060.9660.9910.120.2961.079100
2.93-3.0260.21112230.9770.9940.0940.2311.06100
3.02-3.1360.16312370.9860.9960.0720.1781.05100
3.13-3.2660.11912170.9920.9980.0530.130.982100
3.26-3.4160.09312390.9950.9990.0410.1011.071100
3.41-3.5860.07412200.9950.9990.0330.0811.128100
3.58-3.8160.06712400.9970.9990.030.0731.228100
3.81-4.160.0612450.9950.9990.0270.0651.269100
4.1-4.5260.04112440.99910.0180.0451.02499.9
4.52-5.175.90.03512500.99910.0150.0380.864100
5.17-6.515.90.03812830.99910.0170.0420.786100
6.51-505.40.0313110.99910.0140.0330.77698

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→27.7 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.055 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23793 727 3 %RANDOM
Rwork0.19928 ---
obs0.20042 23892 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.4→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2545 0 1 80 2626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122624
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162375
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.7923574
X-RAY DIFFRACTIONr_angle_other_deg0.4291.7345466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5085339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.11510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27810389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02580
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.172.61356
X-RAY DIFFRACTIONr_mcbond_other2.1682.61356
X-RAY DIFFRACTIONr_mcangle_it3.5484.6561695
X-RAY DIFFRACTIONr_mcangle_other3.5474.6581696
X-RAY DIFFRACTIONr_scbond_it2.5592.7631268
X-RAY DIFFRACTIONr_scbond_other2.5582.7631269
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.94.9821880
X-RAY DIFFRACTIONr_long_range_B_refined6.27323.632621
X-RAY DIFFRACTIONr_long_range_B_other6.29623.62614
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.403→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 38 -
Rwork0.305 1700 -
obs--97.97 %
Refinement TLS params.Method: refined / Origin x: -32.2541 Å / Origin y: -21.067 Å / Origin z: -7.696 Å
111213212223313233
T0.1499 Å20.0025 Å20.0051 Å2-0.0135 Å20.0278 Å2--0.0696 Å2
L2.5913 °20.1291 °20.6093 °2-2.0377 °20.5687 °2--3.4893 °2
S-0.034 Å °0.0896 Å °0.0572 Å °0.2338 Å °-0.057 Å °-0.1917 Å °-0.0009 Å °0.0968 Å °0.091 Å °

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