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- PDB-2gf9: Crystal structure of human RAB3D in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 2gf9
TitleCrystal structure of human RAB3D in complex with GDP
ComponentsRas-related protein Rab-3D
KeywordsPROTEIN TRANSPORT / G-PROTEIN / RAB / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


peptidyl-cysteine methylation / positive regulation of regulated secretory pathway / zymogen granule / secretory vesicle / neutrophil degranulation / GTP-dependent protein binding / RAB geranylgeranylation / myosin V binding / vesicle docking involved in exocytosis / regulation of exocytosis ...peptidyl-cysteine methylation / positive regulation of regulated secretory pathway / zymogen granule / secretory vesicle / neutrophil degranulation / GTP-dependent protein binding / RAB geranylgeranylation / myosin V binding / vesicle docking involved in exocytosis / regulation of exocytosis / azurophil granule membrane / protein secretion / cytoplasmic microtubule / bone resorption / protein localization to plasma membrane / synaptic vesicle / cytoplasmic vesicle / vesicle / endosome / GTPase activity / Neutrophil degranulation / GTP binding / extracellular exosome / plasma membrane
Similarity search - Function
Rab3 / 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
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-3D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 Å
AuthorsHong, B. / Wang, J. / Shen, L. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. ...Hong, B. / Wang, J. / Shen, L. / 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: Crystal structure of human RAB3D in complex with GDP
Authors: Hong, B. / Wang, J. / Shen, L. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionMar 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: 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 ...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
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ACCORDING TO AUTHORS, THE BIOLOGICAL UNIT OF THE PROTEIN IS NOT KNOWN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-3D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1415
Polymers21,6731
Non-polymers4684
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.700, 63.222, 67.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsnot known

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Components

#1: Protein Ras-related protein Rab-3D


Mass: 21673.424 Da / Num. of mol.: 1 / Fragment: residues 20-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB3D, GOV, RAB16 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE-3)-RIL / References: UniProt: O95716
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 1.9 Å3/Da / Density % sol: 30.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG8000, 0.2M magnesium acetate, 0.1M sodium cacodylate, pH 6.5, vapor diffusion, sitting drop, 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: Mar 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.53→28.25 Å / Num. obs: 21079 / % possible obs: 88.3 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.035 / Χ2: 1.56 / Net I/σ(I): 32.8
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
1.53-1.58281.80.0566590.731
1.58-1.6565.52.90.05615380.88
1.65-1.7288.74.20.05520711.114
1.72-1.8199.870.05223481.251
1.81-1.931008.50.04823511.392
1.93-2.081008.60.04223761.512
2.08-2.291008.70.0423571.652
2.29-2.621008.80.03724081.694
2.62-3.291008.80.03424351.803
3.29-3099.18.50.0325361.805

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å28.25 Å
Translation2.5 Å28.25 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3RAB

3rab


Resolution: 1.53→28.25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.164 / SU B: 1.03 / SU ML: 0.04 / ESU R: 0.088 / ESU R Free: 0.087
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ARP/WARP WAS ALSO USED FOR STRUCTURE REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 1069 5.082 %random
Rwork0.1533 ---
all0.155 ---
obs-21035 88.349 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 8.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.293 Å20 Å20 Å2
2--0.166 Å20 Å2
3---0.127 Å2
Refinement stepCycle: LAST / Resolution: 1.53→28.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 31 184 1653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221501
X-RAY DIFFRACTIONr_bond_other_d0.0050.021009
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9672041
X-RAY DIFFRACTIONr_angle_other_deg0.87432443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3825183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99223.86775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.21315256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5151511
X-RAY DIFFRACTIONr_chiral_restr0.0780.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
X-RAY DIFFRACTIONr_nbd_refined0.2130.2267
X-RAY DIFFRACTIONr_nbd_other0.1930.21066
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2759
X-RAY DIFFRACTIONr_nbtor_other0.0850.2754
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2130
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3330.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.228
X-RAY DIFFRACTIONr_mcbond_it1.7562961
X-RAY DIFFRACTIONr_mcbond_other0.4542362
X-RAY DIFFRACTIONr_mcangle_it2.41831429
X-RAY DIFFRACTIONr_scbond_it2.1832698
X-RAY DIFFRACTIONr_scangle_it3.2513608
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 (%)
1.53-1.570.192240.2143500.212173921.507
1.57-1.6130.196490.188750.181168554.837
1.613-1.6590.213640.15811240.161162173.288
1.659-1.710.213660.14513520.148160188.57
1.71-1.7660.178820.14214500.143154499.223
1.766-1.8280.161690.1414350.1411504100
1.828-1.8970.194710.14413710.1461442100
1.897-1.9740.22880.14513180.151406100
1.974-2.0610.193670.14112550.1431322100
2.061-2.1610.164600.14212240.1431284100
2.161-2.2780.173560.1411740.141123199.919
2.278-2.4150.169670.1410980.141116699.914
2.415-2.580.165540.14910520.1491106100
2.58-2.7850.153690.1669520.1651021100
2.785-3.0490.193370.1659110.166948100
3.049-3.4040.192460.1568250.158871100
3.404-3.9220.168270.1517510.15177999.872
3.922-4.7830.232310.1446350.147666100
4.783-6.680.158300.1985070.19653899.814
6.68-300.297120.2223070.22533595.224

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