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- PDB-3c5c: Crystal structure of human Ras-like, family 12 protein in complex... -

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Basic information

Entry
Database: PDB / ID: 3c5c
TitleCrystal structure of human Ras-like, family 12 protein in complex with GDP
ComponentsRAS-like protein 12
KeywordsSIGNALING PROTEIN / ras / rasl12 / gdp / gtpase / Structural Genomics Consortium / SGC / limited proteolysis / GTP-binding / Nucleotide-binding
Function / homology
Function and homology information


small monomeric GTPase / GDP binding / G protein activity / GTPase activity / GTP binding / plasma membrane
Similarity search - Function
: / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...: / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-like protein family member 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsShen, L. / Tong, Y. / Tempel, W. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human Ras-like, family 12 protein in complex with GDP.
Authors: Shen, L. / Tong, Y. / Tempel, W. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionJan 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 21, 2020Group: Data collection / Database references / Derived calculations
Category: pdbx_struct_conn_angle / phasing ...pdbx_struct_conn_angle / phasing / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAS-like protein 12
B: RAS-like protein 12
C: RAS-like protein 12
D: RAS-like protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,66318
Polymers85,7204
Non-polymers1,94314
Water4,017223
1
A: RAS-like protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9225
Polymers21,4301
Non-polymers4924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RAS-like protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9224
Polymers21,4301
Non-polymers4923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RAS-like protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9225
Polymers21,4301
Non-polymers4924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RAS-like protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8984
Polymers21,4301
Non-polymers4683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.040, 66.436, 71.943
Angle α, β, γ (deg.)101.460, 90.030, 89.890
Int Tables number1
Space group name H-MP1
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein
RAS-like protein 12 / RAS-like protein Ris


Mass: 21430.076 Da / Num. of mol.: 4 / Fragment: Residues 18-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RASL12, RIS / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9NYN1
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 1.86 Å3/Da / Density % sol: 33.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 28% PEG 4000, 0.2 M Magnesium chloride. In situ proteolysis with 1:100 endoproteinase Glu-C V8, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 52667 / % possible obs: 98.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.119 / Χ2: 1.501 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.923.90.95550901.26395.6
1.92-1.994.20.69952421.33297.9
1.99-2.084.30.49952131.43998.4
2.08-2.194.30.37452431.42298.7
2.19-2.334.30.31552861.51299.1
2.33-2.514.30.24452981.49699.5
2.51-2.764.40.17853351.48799.7
2.76-3.164.40.10853231.56499.9
3.16-3.984.40.05853241.60899.9
3.98-404.50.04153131.81899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.56 Å
Translation2.5 Å32.56 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.3.0037refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2ATV

2atv


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.186 / SU B: 3.89 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Programs coot, molprobity, ffas03, SCWRL have also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2062 4 %thin shells
Rwork0.202 ---
obs0.203 52136 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0.13 Å20.14 Å2
2--0.4 Å20.01 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5187 0 122 223 5532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215423
X-RAY DIFFRACTIONr_bond_other_d0.0020.023512
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9357394
X-RAY DIFFRACTIONr_angle_other_deg1.0612.9948494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3055675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23523.492252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59415852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4351537
X-RAY DIFFRACTIONr_chiral_restr0.0780.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026042
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021150
X-RAY DIFFRACTIONr_nbd_refined0.2050.21002
X-RAY DIFFRACTIONr_nbd_other0.2030.23620
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22552
X-RAY DIFFRACTIONr_nbtor_other0.0920.22752
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2266
X-RAY DIFFRACTIONr_metal_ion_refined0.0380.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.218
X-RAY DIFFRACTIONr_mcbond_it2.24423392
X-RAY DIFFRACTIONr_mcbond_other0.63621341
X-RAY DIFFRACTIONr_mcangle_it3.04135297
X-RAY DIFFRACTIONr_scbond_it2.2822315
X-RAY DIFFRACTIONr_scangle_it3.1432087
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.89800.3023807394196.6
1.898-1.9500.2513669376697.424
1.95-2.0060.3082920.2363309367897.906
2.006-2.06700.213460352498.184
2.067-2.1350.2572920.2073191353198.641
2.135-2.20900.1983285332998.678
2.209-2.2920.2862840.2082941326298.866
2.292-2.3850.384180.2023021307198.958
2.385-2.4910.2782350.2062789303999.506
2.491-2.6110.2612040.2012631284999.509
2.611-2.75100.2092703271699.521
2.751-2.9170.2581590.2122395255899.844
2.917-3.1160.2151460.2042302245099.918
3.116-3.36300.19922452245100
3.363-3.6790.2311100.1971953206599.903
3.679-4.1060.1971020.1781771187499.947
4.106-4.7260.194570.14916231680100
4.726-5.7530.164490.1881358140999.858
5.753-7.990.241800.21610201100100
7.99-300.19340.197601635100

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