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- PDB-9gh3: pleckstrin homology domain interacting protein with crystallizati... -

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Basic information

Entry
Database: PDB / ID: 9gh3
Titlepleckstrin homology domain interacting protein with crystallization epitope mutations L1408N:R1409E
ComponentsPH-interacting protein
KeywordsPROTEIN BINDING / Crystal Epitopes / Bromodomain
Function / homology
Function and homology information


regulation of cell morphogenesis / positive regulation of insulin-like growth factor receptor signaling pathway / RHOBTB2 GTPase cycle / cytoskeleton organization / positive regulation of mitotic nuclear division / negative regulation of extrinsic apoptotic signaling pathway / lysine-acetylated histone binding / insulin receptor binding / regulation of protein phosphorylation / insulin receptor signaling pathway ...regulation of cell morphogenesis / positive regulation of insulin-like growth factor receptor signaling pathway / RHOBTB2 GTPase cycle / cytoskeleton organization / positive regulation of mitotic nuclear division / negative regulation of extrinsic apoptotic signaling pathway / lysine-acetylated histone binding / insulin receptor binding / regulation of protein phosphorylation / insulin receptor signaling pathway / regulation of cell shape / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
: / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. ...: / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
PH-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsFairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. ...Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A fast, parallel method for efficiently exploring crystallization behaviour of large numbers of protein variants
Authors: Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F.
History
DepositionAug 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PH-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1912
Polymers15,1291
Non-polymers621
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint3 kcal/mol
Surface area8500 Å2
Unit cell
Length a, b, c (Å)83.77, 26.98, 55.83
Angle α, β, γ (deg.)90, 100.56, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PH-interacting protein / PHIP / DDB1- and CUL4-associated factor 14 / IRS-1 PH domain-binding protein / WD repeat-containing protein 11


Mass: 15129.050 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHIP, DCAF14, WDR11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WWQ0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 39.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3000 0.1M citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.16→41.21 Å / Num. obs: 40440 / % possible obs: 94.7 % / Redundancy: 2.7 % / CC1/2: 0.999 / Net I/σ(I): 10.5
Reflection shellResolution: 1.16→1.19 Å / Num. unique obs: 2175 / CC1/2: 0.876

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.77)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→41.21 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.821 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.046 / ESU R Free: 0.048 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2022 1868 4.969 %
Rwork0.1791 35726 -
all0.18 --
obs-37594 94.424 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.842 Å2
Baniso -1Baniso -2Baniso -3
1-0.151 Å20 Å20.738 Å2
2--0.197 Å20 Å2
3----0.582 Å2
Refinement stepCycle: LAST / Resolution: 1.19→41.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 4 220 1277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121140
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.8431547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7265140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.902510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33210203
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.2041059
X-RAY DIFFRACTIONr_chiral_restr0.110.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02889
X-RAY DIFFRACTIONr_nbd_refined0.20.2457
X-RAY DIFFRACTIONr_nbtor_refined0.2970.2768
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2121
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1690.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1990.221
X-RAY DIFFRACTIONr_mcbond_it1.1781.426545
X-RAY DIFFRACTIONr_mcangle_it1.5982.59690
X-RAY DIFFRACTIONr_scbond_it2.7811.755595
X-RAY DIFFRACTIONr_scangle_it4.043.111857
X-RAY DIFFRACTIONr_lrange_it5.5223.7721800
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.19-1.2210.3291110.3123940.31129310.9150.91985.46570.299
1.221-1.2540.3271100.30921470.30928000.9140.92480.60710.302
1.254-1.2910.2871280.26822920.26928140.9390.94385.99860.257
1.291-1.330.2081320.24722310.24426530.9650.95389.0690.228
1.33-1.3740.2431320.22224290.22326020.9560.96598.42430.198
1.374-1.4220.2311080.20724080.20825620.9690.9798.20450.185
1.422-1.4760.2231150.19322590.19424230.970.97597.97770.17
1.476-1.5360.1891150.1721710.17123330.9760.9897.98540.152
1.536-1.6040.1821050.15920940.16122460.9770.98497.90740.143
1.604-1.6820.1841020.15520460.15721730.9790.98498.84950.144
1.682-1.7730.1871090.16118830.16320430.9760.98397.50370.151
1.773-1.880.168990.16618250.16619480.980.98298.7680.156
1.88-2.010.1971000.16517120.16718400.9770.98398.47830.159
2.01-2.1710.165890.15915710.15916980.9840.98697.76210.16
2.171-2.3770.2740.16614780.16815830.9750.98498.04170.171
2.377-2.6570.181690.17213580.17214470.9810.98298.61780.181
2.657-3.0650.192660.17411800.17512720.9750.98197.9560.191
3.065-3.7490.212480.1629840.16410770.9720.98395.82170.186
3.749-5.280.208420.1628000.1648660.9790.98397.22860.191
5.28-41.210.249140.2114630.2125010.970.97395.20960.267

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