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- PDB-2ocb: Crystal structure of human RAB9B in complex with a GTP analogue -

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Basic information

Entry
Database: PDB / ID: 2ocb
TitleCrystal structure of human RAB9B in complex with a GTP analogue
ComponentsRas-related protein Rab-9B
KeywordsTRANSPORT PROTEIN / G-PROTEIN / RAB / GTPASE / GTP ANALOGUE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Rab protein signal transduction / Retrograde transport at the Trans-Golgi-Network / RAB geranylgeranylation / RHOBTB3 ATPase cycle / RAB GEFs exchange GTP for GDP on RABs / retrograde transport, endosome to Golgi / phagocytic vesicle / secretory granule membrane / phagocytic vesicle membrane / GDP binding ...Rab protein signal transduction / Retrograde transport at the Trans-Golgi-Network / RAB geranylgeranylation / RHOBTB3 ATPase cycle / RAB GEFs exchange GTP for GDP on RABs / retrograde transport, endosome to Golgi / phagocytic vesicle / secretory granule membrane / phagocytic vesicle membrane / GDP binding / protein transport / late endosome / lysosome / GTPase activity / Neutrophil degranulation / GTP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Rab9 / 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 / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...Rab9 / 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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-9B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsHong, B. / Shen, L. / Walker, J.R. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. ...Hong, B. / Shen, L. / Walker, J.R. / 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 RAB9B in complex with a GTP analogue
Authors: Hong, B. / Shen, L. / Walker, J.R. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionDec 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 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 ...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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). 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-9B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,10910
Polymers20,5631
Non-polymers5479
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.430, 70.430, 97.715
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailsnot known

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Components

#1: Protein Ras-related protein Rab-9B / Rab-9L / RAB9-like protein


Mass: 20562.881 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB9B, RAB9L / Plasmid: pET28aLIc / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon plus / References: UniProt: Q9NP90
#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


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.5 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M ammonium sulfate, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, hanging drop, 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: Aug 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 14718 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.107 / Χ2: 1.934 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
2.2-2.281005.80.72514401.797
2.28-2.371006.10.61314431.56
2.37-2.481006.20.59814511.58
2.48-2.611006.20.41514411.564
2.61-2.771006.20.3314561.759
2.77-2.991006.20.24214561.817
2.99-3.291006.20.1414732.112
3.29-3.761006.20.0914772.516
3.76-4.731006.20.05915032.553
4.73-3099.45.90.04215782.022

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.2 Å29.77 Å
Translation3.2 Å29.77 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
ARP/wARPmodel building
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1wms

1wms


Resolution: 2.2→23.051 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.195 / SU B: 5.962 / SU ML: 0.151 / ESU R: 0.201 / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 738 5.032 %random
Rwork0.2135 ---
all0.215 ---
obs-14665 99.83 %-
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: 31.515 Å2
Baniso -1Baniso -2Baniso -3
1-2.436 Å21.218 Å20 Å2
2--2.436 Å20 Å2
3----3.654 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 0 40 37 1445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221437
X-RAY DIFFRACTIONr_bond_other_d0.0020.02921
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9671958
X-RAY DIFFRACTIONr_angle_other_deg0.9532240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51524.78971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57915222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.395157
X-RAY DIFFRACTIONr_chiral_restr0.0760.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02301
X-RAY DIFFRACTIONr_nbd_refined0.1820.2295
X-RAY DIFFRACTIONr_nbd_other0.1960.2941
X-RAY DIFFRACTIONr_nbtor_refined0.180.2664
X-RAY DIFFRACTIONr_nbtor_other0.0840.2749
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.22
X-RAY DIFFRACTIONr_mcbond_it2.7292956
X-RAY DIFFRACTIONr_mcbond_other0.7012355
X-RAY DIFFRACTIONr_mcangle_it3.79231388
X-RAY DIFFRACTIONr_scbond_it2.3992650
X-RAY DIFFRACTIONr_scangle_it3.1853568
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 (%)
2.2-2.2570.355610.39980.303106199.812
2.257-2.3180.399670.2899470.296101699.803
2.318-2.3850.288490.2839540.283100699.702
2.385-2.4570.404440.2919290.29697699.693
2.457-2.5370.294530.2539000.25595499.895
2.537-2.6250.334540.2398700.24592599.892
2.625-2.7230.291380.2398390.24288199.546
2.723-2.8320.3410.2388140.24185699.883
2.832-2.9560.298420.2367970.23984199.762
2.956-3.0980.28230.2157590.21778399.872
3.098-3.2620.2410.2187060.21774899.866
3.262-3.4560.263370.2096850.21272399.862
3.456-3.6880.214300.26390.20167099.851
3.688-3.9750.201420.185980.182640100
3.975-4.3420.266230.1725700.17559499.832
4.342-4.8330.16250.1565090.15753599.813
4.833-5.540.232260.1794650.182491100
5.54-6.690.173180.2273960.224414100
6.69-9.0860.382100.2083340.211344100
9.086-23.0510.211140.2182180.218232100

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