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- PDB-9ejp: Crystal structure of WDR91 in complex with XS838489 -

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Basic information

Entry
Database: PDB / ID: 9ejp
TitleCrystal structure of WDR91 in complex with XS838489
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 / phosphatidylinositol 3-kinase regulator activity / early endosome to late endosome transport / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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 XS838489
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)41,4483
Polymers41,0641
Non-polymers3832
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.613, 132.547, 119.797
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-A1BIW / N-[(5R)-1,1-dioxo-2,3,4,5-tetrahydro-1H-1lambda~6~-benzothiepin-5-yl]-2-hydroxyquinoxaline-6-carboxamide


Mass: 383.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17N3O4S / 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.: 93 / 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: 3.75 Å3/Da / Density % sol: 67.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02M of each alcohol, 0.1M MOPS/HEPES-Na pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 30949 / % possible obs: 100 % / Redundancy: 10.8 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.019 / Rrim(I) all: 0.065 / Χ2: 0.828 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2.22-2.2610.80.90415340.8020.9430.2860.9490.977
2.26-2.3110.87414990.8460.9570.2730.9170.975
2.3-2.3411.10.77115280.8710.9650.2390.8080.937
2.34-2.3911.10.66915330.910.9760.2080.7010.919
2.39-2.4411.10.56215180.9270.9810.1750.5890.907
2.44-2.5110.48215440.9440.9860.150.5050.913
2.5-2.56110.38815220.960.990.1210.4070.883
2.56-2.6310.90.32115330.9730.9930.1010.3360.852
2.63-2.7110.60.24915170.9810.9950.0790.2620.845
2.71-2.89.80.215620.9870.9970.0670.2110.883
2.8-2.99.90.15515260.9920.9980.0520.1640.851
2.9-3.0110.30.13315280.9940.9980.0430.140.832
3.01-3.1510.40.09415550.9970.9990.030.0990.745
3.15-3.3211.60.07315490.99810.0220.0760.663
3.32-3.5211.50.05115460.99910.0160.0540.544
3.52-3.811.50.04315530.99910.0130.0450.674
3.8-4.1811.10.0341565110.010.0350.854
4.18-4.7810.50.0261577110.0080.0280.863
4.78-6.029.70.0261586110.0090.0270.776
6.02-5011.10.02216740.99910.0070.0240.714

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→44.69 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.871 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24497 1573 5.1 %RANDOM
Rwork0.20262 ---
obs0.2047 29329 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.285 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20 Å20 Å2
2---0.93 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 2.22→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2535 0 1 93 2629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122648
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162406
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.7943609
X-RAY DIFFRACTIONr_angle_other_deg0.4711.7425525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4945344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.567514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38210399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023221
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02605
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_it3.5784.6871370
X-RAY DIFFRACTIONr_mcbond_other3.5724.6871370
X-RAY DIFFRACTIONr_mcangle_it5.4868.3871716
X-RAY DIFFRACTIONr_mcangle_other5.4858.3911717
X-RAY DIFFRACTIONr_scbond_it3.884.9441278
X-RAY DIFFRACTIONr_scbond_other3.8794.9451279
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0068.9561894
X-RAY DIFFRACTIONr_long_range_B_refined8.49842.032683
X-RAY DIFFRACTIONr_long_range_B_other8.50642.032672
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.22→2.276 Å
RfactorNum. reflection% reflection
Rfree0.313 108 -
Rwork0.294 2086 -
obs--98.12 %

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