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- PDB-2ew1: Crystal Structure of Rab30 in complex with a GTP analogue -

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Basic information

Entry
Database: PDB / ID: 2ew1
TitleCrystal Structure of Rab30 in complex with a GTP analogue
ComponentsRas-related protein Rab-30
KeywordsSIGNALING PROTEIN / G-protein / RAB / GTP analogue / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Rab protein signal transduction / Golgi cisterna / Intra-Golgi traffic / Golgi stack / RAB geranylgeranylation / cis-Golgi network / Golgi organization / trans-Golgi network / Golgi membrane / intracellular membrane-bounded organelle ...Rab protein signal transduction / Golgi cisterna / Intra-Golgi traffic / Golgi stack / RAB geranylgeranylation / cis-Golgi network / Golgi organization / trans-Golgi network / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / GTP binding
Similarity search - Function
Rab30 / small GTPase Rab1 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 / Ras-related protein Rab-30
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, J. / Shen, Y. / Ismail, S. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Bochkarev, A. / Park, H.W. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of RAB30 in complex with a GTP analogue
Authors: Wang, J. / Shen, Y. / Ismail, S. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Bochkarev, A. / Park, H.W.
History
DepositionNov 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4283
Polymers22,8821
Non-polymers5472
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.002, 57.955, 82.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ras-related protein Rab-30


Mass: 22881.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB30 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q15771
#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.: 106 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4K, 0.2M MgCl2, 0.1 M Tris-HCl 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 14546 / Num. obs: 14546 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Rsym value: 0.088 / Net I/σ(I): 47.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 10.13 / Num. unique all: 1433 / Rsym value: 0.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YU9.pdb

1yu9


Resolution: 2→47.51 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.265 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.212 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28423 727 5 %RANDOM
Rwork0.23406 ---
obs0.23662 13738 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.986 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2---1.08 Å20 Å2
3---1.68 Å2
Refinement stepCycle: LAST / Resolution: 2→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 33 106 1517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221434
X-RAY DIFFRACTIONr_angle_refined_deg2.1161.991942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.825170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47524.08571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.56615256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1041512
X-RAY DIFFRACTIONr_chiral_restr0.1760.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021067
X-RAY DIFFRACTIONr_nbd_refined0.2510.2682
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2958
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.296
X-RAY DIFFRACTIONr_metal_ion_refined0.0210.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.22
X-RAY DIFFRACTIONr_mcbond_it1.3541.5874
X-RAY DIFFRACTIONr_mcangle_it2.03221366
X-RAY DIFFRACTIONr_scbond_it3.2973652
X-RAY DIFFRACTIONr_scangle_it4.9254.5576
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 54 -
Rwork0.264 981 -
obs--99.42 %

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