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- PDB-2p5s: RAB domain of human RASEF in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 2p5s
TitleRAB domain of human RASEF in complex with GDP
ComponentsRAS and EF-hand domain containing
KeywordsSIGNALING PROTEIN / G-PROTEIN / RAB / GDP / STRUCTURAL GENOMICS / SGC / Structural Genomics Consortium
Function / homology
Function and homology information


vesicle-mediated transport / GDP binding / GTPase activity / calcium ion binding / GTP binding / perinuclear region of cytoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / EF-hand domain pair / Rab subfamily of small GTPases / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / EF-hand domain pair / Rab subfamily of small GTPases / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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
GUANOSINE-5'-DIPHOSPHATE / Ras and EF-hand domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsZhu, H. / Wang, J. / Shen, Y. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. ...Zhu, H. / Wang, J. / Shen, Y. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: RAB domain of human RASEF in complex with GDP
Authors: Zhu, H. / Wang, J. / Shen, Y. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionMar 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAS and EF-hand domain containing
B: RAS and EF-hand domain containing
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0177
Polymers44,1312
Non-polymers8865
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-21 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.275, 42.524, 75.656
Angle α, β, γ (deg.)90.00, 98.91, 90.00
Int Tables number4
Space group name H-MP1211
Detailsnot known

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Components

#1: Protein RAS and EF-hand domain containing


Mass: 22065.264 Da / Num. of mol.: 2 / Fragment: residues 533-712
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RASEF / Plasmid: pET28a-LIC-Thrombin / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon(+) RIL / References: UniProt: Q8IZ41
#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-UNX / UNKNOWN ATOM OR ION


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


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 20% PEG-3350, 0.2M KF, vapor diffusion, sitting drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Nov 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 29262 / % possible obs: 94.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.077 / Χ2: 1.07 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
2-2.0769.51.90.75121250.947
2.07-2.1585.32.40.61125940.939
2.15-2.2595.72.90.48729281.083
2.25-2.3798.93.50.42430401.038
2.37-2.521003.70.30130490.945
2.52-2.711003.70.22130680.978
2.71-2.991003.70.12230770.945
2.99-3.4299.93.70.0730741.181
3.42-4.311003.70.03931061.167
4.31-5099.83.60.03232011.315

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å36.96 Å
Translation2.5 Å36.96 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1g16

1g16


Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.195 / SU B: 5.428 / SU ML: 0.142 / ESU R: 0.204 / ESU R Free: 0.189
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. arp/warp, molprobity, coot were also used for the refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2602 1377 5.617 %thin shells
Rwork0.2111 ---
all0.214 ---
obs-24513 99.106 %-
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: 27.035 Å2
Baniso -1Baniso -2Baniso -3
1--0.075 Å20 Å20.194 Å2
2--0.951 Å20 Å2
3----0.816 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 59 38 2527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222524
X-RAY DIFFRACTIONr_bond_other_d0.0020.021679
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9873409
X-RAY DIFFRACTIONr_angle_other_deg0.92434091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8015312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54724.059101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01715438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8771514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02516
X-RAY DIFFRACTIONr_nbd_refined0.2110.2427
X-RAY DIFFRACTIONr_nbd_other0.1840.21641
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21182
X-RAY DIFFRACTIONr_nbtor_other0.0840.21254
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.22
X-RAY DIFFRACTIONr_mcbond_it2.91121759
X-RAY DIFFRACTIONr_mcbond_other0.6472653
X-RAY DIFFRACTIONr_mcangle_it3.72332489
X-RAY DIFFRACTIONr_scbond_it2.44721082
X-RAY DIFFRACTIONr_scangle_it3.3543920
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.15-2.2050.3331880.27714860.283177594.31
2.205-2.26500.28116930.281175096.743
2.265-2.330.3221840.27615000.282171198.422
2.33-2.400.24516360.245164199.695
2.4-2.4780.3031520.24414680.25162599.692
2.478-2.56300.25715360.257154299.611
2.563-2.6580.2831400.22313880.2281528100
2.658-2.7650.277980.22213260.226142599.93
2.765-2.8850.39550.22213780.222138599.856
2.885-3.0230.3081110.2212380.227135099.926
3.023-3.1830.2491000.21211680.215127599.451
3.183-3.3700.20112010.2011201100
3.37-3.5960.25730.19910780.202115299.913
3.596-3.8730.249760.1889750.192105299.905
3.873-4.2270.263590.1789330.18299499.799
4.227-4.70.134470.1648400.16289099.663
4.7-5.3780.265520.1747600.179812100
5.378-6.4710.242300.2296520.229682100
6.471-8.7070.224400.2065360.208576100
8.707-200.24220.2193440.2236899.457

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