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- PDB-4ku4: Crystal Structure of a Ras-like Protein from Cryphonectria parasi... -

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Basic information

Entry
Database: PDB / ID: 4ku4
TitleCrystal Structure of a Ras-like Protein from Cryphonectria parasitica in Complex with GDP
ComponentsRas-3 from Cryphonectria parasitica
KeywordsSIGNALING PROTEIN / small G protein / GTP/GDP binding / GTP hydrolysis
Function / homologyP-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / GUANOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChen, C.
CitationJournal: To be Published
Title: Crystal Structure of a Ras-like Protein from Cryphonectria parasitica in Complex with GDP
Authors: Chen, C. / Choi, G.
History
DepositionMay 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-3 from Cryphonectria parasitica
B: Ras-3 from Cryphonectria parasitica
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2157
Polymers46,2562
Non-polymers9595
Water13,367742
1
A: Ras-3 from Cryphonectria parasitica
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6204
Polymers23,1281
Non-polymers4923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ras-3 from Cryphonectria parasitica
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5963
Polymers23,1281
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.795, 52.595, 53.234
Angle α, β, γ (deg.)114.62, 93.01, 90.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ras-3 from Cryphonectria parasitica


Mass: 23128.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryphonectria parasitica (chestnut blight fungus)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 742 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5 mM GDP, 0.2 M Magnesium Format, 0.1 M HEPES, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→44.51 Å / Num. all: 48257 / Num. obs: 42642 / % possible obs: 88.4 % / Observed criterion σ(F): 2.15 / Observed criterion σ(I): 2.9 / Redundancy: 3.5 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 11.07
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 2.74 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3545 / Rsym value: 0.313 / % possible all: 62.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CE2

2ce2


Resolution: 1.6→44.5 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2.15 / Phase error: 22.33 / Stereochemistry target values: ML / Details: Anisotropic B factors came from TLS refinememnt
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 2162 5.08 %random
Rwork0.1925 ---
obs0.194 42577 89.08 %-
all-48257 --
Solvent computationShrinkage radii: 0.05 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.296 Å2 / ksol: 0.464 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.3797 Å20.0644 Å20.0992 Å2
2--0.34 Å2-2.7349 Å2
3---1.0398 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2686 0 59 742 3487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092794
X-RAY DIFFRACTIONf_angle_d1.223769
X-RAY DIFFRACTIONf_dihedral_angle_d15.0661059
X-RAY DIFFRACTIONf_chiral_restr0.075431
X-RAY DIFFRACTIONf_plane_restr0.004478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.63720.31491110.24832019X-RAY DIFFRACTION67
1.6372-1.67820.28631390.25052530X-RAY DIFFRACTION83
1.6782-1.72350.28591400.23712554X-RAY DIFFRACTION86
1.7235-1.77430.27841280.22752614X-RAY DIFFRACTION85
1.7743-1.83150.26291420.22532616X-RAY DIFFRACTION86
1.8315-1.8970.23821410.21452686X-RAY DIFFRACTION89
1.897-1.97290.22951450.19282683X-RAY DIFFRACTION89
1.9729-2.06270.24611350.18262744X-RAY DIFFRACTION90
2.0627-2.17150.231480.18162754X-RAY DIFFRACTION92
2.1715-2.30750.2091540.17252806X-RAY DIFFRACTION93
2.3075-2.48570.22251740.18052816X-RAY DIFFRACTION94
2.4857-2.73580.21621420.19362838X-RAY DIFFRACTION94
2.7358-3.13160.20791650.18982875X-RAY DIFFRACTION95
3.1316-3.94510.18081560.16982913X-RAY DIFFRACTION96
3.9451-44.52710.20021420.19062967X-RAY DIFFRACTION97
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.26970.27380.10080.1213-0.01090.0206-0.01010.0327-0.0189-0.02280.0032-0.0004-0.0112-0.00240.05950.00550.0060.0615-0.00110.053813.058243.68817.1716
20.2956-0.10160.00870.09180.02220.1058-0.0015-0.00890.01340.0223-0.00460.00160.0107-0.01880.0596-0.0013-0.00230.0546-0.00160.0497-5.431712.037526.5028
30.1030.0566-0.03980.07660.05490.0871-0.00010.0007-0.0067-0.00750.0003-0.0047-0.01060.00150.0466-0.003-0.00970.03380.0050.04254.092627.140316.5326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 7:195)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 6:194)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 301:769) OR CHAIN B AND (RESSEQ 600:1073)

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