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- PDB-3oes: Crystal structure of the small GTPase RhebL1 -

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Basic information

Entry
Database: PDB / ID: 3oes
TitleCrystal structure of the small GTPase RhebL1
ComponentsGTPase RhebL1
KeywordsHYDROLASE / small gtpase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


small GTPase-mediated signal transduction / TOR signaling / endomembrane system / GDP binding / positive regulation of NF-kappaB transcription factor activity / GTPase activity / GTP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase RhebL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.301 Å
AuthorsNedyalkova, L. / Zhong, N. / Tempel, W. / Tong, Y. / Shen, L. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Nedyalkova, L. / Zhong, N. / Tempel, W. / Tong, Y. / Shen, L. / 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 the small GTPase RhebL1
Authors: Nedyalkova, L. / Zhong, N. / Tempel, W. / Tong, Y. / Shen, L. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionAug 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_ref_seq_dif / 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_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.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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTPase RhebL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4553
Polymers22,9091
Non-polymers5472
Water23413
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.665, 126.745, 41.356
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsThe authors state that the biological unit is unknown.

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Components

#1: Protein GTPase RhebL1 / Ras homolog enriched in brain-like protein 1 / Rheb-like protein 1 / Rheb2 / Ras homolog enriched ...Ras homolog enriched in brain-like protein 1 / Rheb-like protein 1 / Rheb2 / Ras homolog enriched in brain like-1 c / RhebL1c


Mass: 22908.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHEBL1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q8TAI7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.08 Å3/Da / Density % sol: 40.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 9.5
Details: 1.8M sodium formate, 0.1M lysine buffer, pH 9.5, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 8829 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.105 / Χ2: 1.79 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.346.80.854251.633100
2.34-2.3870.7454251.713100
2.38-2.4370.7144421.728100
2.43-2.4870.6634261.639100
2.48-2.5370.5884411.677100
2.53-2.597.10.4514301.737100
2.59-2.667.10.4554251.651100
2.66-2.7370.4414431.77100
2.73-2.8170.374431.798100
2.81-2.97.10.2894381.77100
2.9-37.10.2384351.767100
3-3.127.10.1794271.777100
3.12-3.267.10.1534341.851100
3.26-3.447.10.1184521.889100
3.44-3.657.10.094441.895100
3.65-3.9370.0754412.078100
3.93-4.3370.0564471.84100
4.33-4.9570.0454551.807100
4.95-6.246.80.0494591.803100
6.24-506.20.044971.95598.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.005data extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1xtr

1xtr


Resolution: 2.301→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.192 / SU B: 7.291 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. Programs chainsaw, coot and the molprobity server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 418 4.766 %RANDOM
Rwork0.212 ---
obs0.215 8770 99.523 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.946 Å2
Baniso -1Baniso -2Baniso -3
1--1.669 Å20 Å20 Å2
2--3.182 Å20 Å2
3----1.513 Å2
Refinement stepCycle: LAST / Resolution: 2.301→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 0 33 13 1241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221252
X-RAY DIFFRACTIONr_bond_other_d0.0020.02795
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9821705
X-RAY DIFFRACTIONr_angle_other_deg0.8631946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9285154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.48324.31451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71315193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.669154
X-RAY DIFFRACTIONr_chiral_restr0.0710.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021371
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02248
X-RAY DIFFRACTIONr_mcbond_it0.7521.5775
X-RAY DIFFRACTIONr_mcbond_other0.1111.5320
X-RAY DIFFRACTIONr_mcangle_it1.47421241
X-RAY DIFFRACTIONr_scbond_it1.9813477
X-RAY DIFFRACTIONr_scangle_it3.324.5464
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 (%)
2.301-2.360.263300.26959363098.889
2.36-2.4240.302440.24756661299.673
2.424-2.4930.214210.2556558999.491
2.493-2.5690.363320.23955859399.494
2.569-2.6520.257290.24152955999.821
2.652-2.7430.317290.24552555599.82
2.743-2.8440.325200.22450052499.237
2.844-2.9580.281220.22649752598.857
2.958-3.0860.26220.2346849399.391
3.086-3.2330.303290.20244547699.58
3.233-3.4030.282170.20942744599.775
3.403-3.6030.228190.18941243399.538
3.603-3.8430.213190.199389408100
3.843-4.1380.172160.18635937799.469
4.138-4.5140.248180.167338356100
4.514-5.0150.252180.18630632599.692
5.015-5.7310.341110.20627929199.656
5.731-6.8790.36180.2625726699.624
6.879-9.20.28560.2120020899.038
9.2-200.31880.234139147100

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