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- PDB-8ebz: Crystal Structure of GMPPNP-bound KRAS-G13D mutant at 1.2 Ang res... -

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Basic information

Entry
Database: PDB / ID: 8ebz
TitleCrystal Structure of GMPPNP-bound KRAS-G13D mutant at 1.2 Ang resolution
ComponentsIsoform 2B of GTPase KRas
KeywordsONCOPROTEIN / KRAS / K-RAS / mutant / cancer / RAS / small GTPase / GMPPNP / GppNHp / G13D / hydrolase
Function / homologysmall monomeric GTPase / Ca2+ pathway / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Isoform 2B of GTPase KRas
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsChan, A.H. / Simanshu, D.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
CitationJournal: Commun Biol / Year: 2023
Title: Reduced dynamic complexity allows structure elucidation of an excited state of KRAS G13D .
Authors: Chao, F.A. / Chan, A.H. / Dharmaiah, S. / Schwieters, C.D. / Tran, T.H. / Taylor, T. / Ramakrishnan, N. / Esposito, D. / Nissley, D.V. / McCormick, F. / Simanshu, D.K. / Cornilescu, G.
History
DepositionAug 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0226
Polymers19,4031
Non-polymers6195
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.930, 38.230, 36.320
Angle α, β, γ (deg.)90.000, 103.280, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-398-

HOH

21A-483-

HOH

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Components

#1: Protein Isoform 2B of GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 19402.848 Da / Num. of mol.: 1 / Mutation: G13D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116-2, small monomeric GTPase
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.59 % / Description: 3D rectangle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 20% PEG 400, 20% PEG 8000, 50 mM Magnesium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.2→35.349 Å / Num. obs: 48372 / % possible obs: 95.3 % / Redundancy: 5.724 % / Biso Wilson estimate: 12.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.049 / Χ2: 1.053 / Net I/σ(I): 20.33 / Num. measured all: 276904
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.2-1.235.4980.1887.6918318373233320.9830.20889.3
1.23-1.265.6850.1688.5918759364133000.9870.18590.6
1.26-1.35.4140.1499.2717618352532540.9860.16592.3
1.3-1.345.3630.12910.6217214343332100.9910.14393.5
1.34-1.396.0240.11112.818679332931010.9940.12293.2
1.39-1.435.9750.10214.218092321130280.9940.11294.3
1.43-1.495.7970.08616.1417066311129440.9940.09494.6
1.49-1.555.8680.07518.817159301729240.9960.08296.9
1.55-1.625.7750.0720.9516042284127780.9960.07797.8
1.62-1.75.6610.06323.2715455277527300.9960.06998.4
1.7-1.795.2740.05524.6613095260324830.9960.06195.4
1.79-1.96.0790.04928.8915112250724860.9980.05499.2
1.9-2.036.0420.04631.5614042234423240.9980.0599.1
2.03-2.195.8390.04532.4512560216421510.9980.04999.4
2.19-2.45.8080.04433.0911576200119930.9970.04899.6
2.4-2.685.7210.04233.3910310181718020.9980.04699.2
2.68-3.15.3510.0432.758502162015890.9970.04598.1
3.1-3.795.8410.03935.187588138112990.9980.04394.1
3.79-5.376.0710.03836.086441106610610.9980.04299.5
5.37-35.3495.6190.03734.4632766155830.9960.04194.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GFT

3gft


Resolution: 1.2→35.349 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1709 4867 10.06 %Random
Rwork0.1591 43497 --
obs0.1603 48364 95.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.1 Å2 / Biso mean: 20.6357 Å2 / Biso min: 8.41 Å2
Refinement stepCycle: final / Resolution: 1.2→35.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1346 0 36 186 1568
Biso mean--10.21 30.44 -
Num. residues----170
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.2-1.21360.21421410.1893133690
1.2136-1.22790.21961580.1864136489
1.2279-1.24280.20441560.1854138390
1.2428-1.25860.20551520.1803132791
1.2586-1.27510.19151570.1812134391
1.2751-1.29260.21371690.1798143894
1.2926-1.31110.19891410.1743141193
1.3111-1.33060.2091550.1788139494
1.3306-1.35140.19971480.1782145893
1.3514-1.37360.17921660.174137993
1.3736-1.39730.19891680.1726142594
1.3973-1.42270.23961300.169143594
1.4227-1.450.20051610.1731142895
1.45-1.47960.18381690.1676141294
1.4796-1.51180.1741620.1673149997
1.5118-1.5470.19361600.1692146197
1.547-1.58570.18211770.1616145397
1.5857-1.62850.19031530.1586150199
1.6285-1.67650.1671890.1588146998
1.6765-1.73060.16291530.1608150297
1.7306-1.79240.20581720.1653140695
1.7924-1.86420.17981610.1654153599
1.8642-1.9490.17021660.1618150899
1.949-2.05180.14941710.1505153499
2.0518-2.18030.17871730.15881512100
2.1803-2.34860.1631620.1556153899
2.3486-2.58490.18631790.16231502100
2.5849-2.95880.17731690.17152899
2.9588-3.72710.14451710.1421145594
3.7271-35.3490.14641780.1454156198
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)
10.58570.39090.06690.26590.39310.45150.1109-0.0687-0.14460.0819-0.0859-0.09190.14120.0115-0.00560.1418-0.013-0.01050.08950.01990.1294-25.5002-21.410811.9526
2-0.0229-0.0192-0.10020.2106-0.00840.1909-0.04910.00920.0166-0.0772-0.02610.30520.018-0.14020.0070.14580.0147-0.00680.1226-0.00160.1957-35.7314-17.43044.2289
30.1420.2141-0.1160.18070.02630.32840.04010.0434-0.1858-0.2487-0.06030.2293-0.00460.05120.00160.130.014400.10210.00780.1945-26.1858-24.905515.5829
40.68430.0341-0.3150.32480.00810.3670.0988-0.08830.1059-0.3599-0.07480.1059-0.14140.21720.03020.2053-0.01180.00840.1231-0.00130.1336-25.2771-7.205619.1947
50.05560.0663-0.01580.19980.13230.1112-0.0078-0.03080.02540.04280.0054-0.0338-0.25280.16620.00350.0985-0.00120.00260.12-0.00260.0891-18.4316-14.52647.4961
60.91360.0735-0.18140.60980.06450.28710.0015-0.0357-0.0093-0.02640.0484-0.0938-0.03360.22040.01410.1018-0.0090.00380.1399-0.00590.1056-14.812-11.3048.1274
70.21080.14890.19090.2238-0.08461.05360.23790.0994-0.18860.05780.0981-0.2365-0.16880.39680.07580.12140.01690.00090.3076-0.01320.1577-6.0432-14.25173.4191
80.05380.09850.00970.0327-0.1240.15940.05610.0613-0.17720.04950.0302-0.02090.16770.1950.00140.12090.0144-0.01540.1374-0.01510.131-17.9624-22.22031.6551
90.113-0.0418-0.03550.4571-0.15510.10840.1718-0.1485-0.2899-0.0137-0.1136-0.08350.29690.1372-0.02730.14020.0223-0.03530.20050.01710.1803-14.2066-26.757414.7528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 25 )A0 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 36 )A26 - 36
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 61 )A37 - 61
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 74 )A62 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 86 )A75 - 86
6X-RAY DIFFRACTION6chain 'A' and (resid 87 through 126 )A87 - 126
7X-RAY DIFFRACTION7chain 'A' and (resid 127 through 137 )A127 - 137
8X-RAY DIFFRACTION8chain 'A' and (resid 138 through 151 )A138 - 151
9X-RAY DIFFRACTION9chain 'A' and (resid 152 through 169 )A152 - 169

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