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- PDB-2g6b: Crystal structure of human RAB26 in complex with a GTP analogue -

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Basic information

Entry
Database: PDB / ID: 2g6b
TitleCrystal structure of human RAB26 in complex with a GTP analogue
ComponentsRas-related protein Rab-26
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / G-PROTEIN / RAB / GTP ANALOGUE / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


exocrine system development / GMP binding / regulation protein catabolic process at presynapse / regulated exocytosis / regulation of exocytosis / RAB geranylgeranylation / Golgi to plasma membrane protein transport / secretory granule membrane / synaptic vesicle membrane / endosome ...exocrine system development / GMP binding / regulation protein catabolic process at presynapse / regulated exocytosis / regulation of exocytosis / RAB geranylgeranylation / Golgi to plasma membrane protein transport / secretory granule membrane / synaptic vesicle membrane / endosome / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / plasma membrane
Similarity search - Function
ARF-like small GTPases; ARF, ADP-ribosylation factor / 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 ...ARF-like small GTPases; ARF, ADP-ribosylation factor / 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-26
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsWang, J. / Tempel, W. / Shen, Y. / Shen, L. / Yaniw, D. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. ...Wang, J. / Tempel, W. / Shen, Y. / Shen, L. / Yaniw, D. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human RAB26 in complex with a GTP analogue
Authors: Wang, J. / Tempel, W. / Shen, Y. / Shen, L. / Yaniw, D. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionFeb 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 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 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
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 MOLECULE FOR THE PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab-26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6427
Polymers20,0951
Non-polymers5476
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.368, 55.614, 92.300
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-26


Mass: 20095.055 Da / Num. of mol.: 1 / Fragment: residues 56-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB26 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE-3)-RIL / References: UniProt: Q9ULW5
#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.: 4 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.4 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG3350, 0.1M NH4SO4, 0.1M HEPES, pH 7.5, 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: Feb 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 12581 / % possible obs: 99.5 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.173 / Χ2: 1.017 / Net I/σ(I): 4.4
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
2-2.0795.76.30.84111780.863
2.07-2.1599.37.20.71612240.866
2.15-2.251007.70.60312400.923
2.25-2.3799.97.80.49512310.903
2.37-2.521007.80.4412530.927
2.52-2.711007.90.35812500.909
2.71-2.991007.90.23512591.042
2.99-3.421007.90.13912771.122
3.42-4.311007.80.08812861.274
4.31-301007.40.06813831.262

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å19.58 Å
Translation2.5 Å19.58 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 1G16_A

Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.888 / WRfactor Rfree: 0.236 / WRfactor Rwork: 0.181 / SU B: 4.67 / SU ML: 0.133 / ESU R: 0.198 / ESU R Free: 0.192
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ARP/wARP was also used for the refinement.
RfactorNum. reflection% reflection
Rfree0.2769 609 4.876 %
Rwork0.2096 --
all0.213 --
obs-12491 99.673 %
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: 19.721 Å2
Baniso -1Baniso -2Baniso -3
1-0.059 Å20 Å20 Å2
2--0.615 Å20 Å2
3----0.674 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 37 62 1371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221331
X-RAY DIFFRACTIONr_bond_other_d0.0020.02865
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9841810
X-RAY DIFFRACTIONr_angle_other_deg1.01832117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27924.38657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78215226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.854156
X-RAY DIFFRACTIONr_chiral_restr0.080.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021469
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02271
X-RAY DIFFRACTIONr_nbd_refined0.20.3261
X-RAY DIFFRACTIONr_nbd_other0.2090.3890
X-RAY DIFFRACTIONr_nbtor_refined0.1770.5612
X-RAY DIFFRACTIONr_nbtor_other0.0870.5672
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.5123
X-RAY DIFFRACTIONr_metal_ion_refined0.0270.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.35
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.316
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3110.57
X-RAY DIFFRACTIONr_mcbond_it2.3672839
X-RAY DIFFRACTIONr_mcbond_other0.5582340
X-RAY DIFFRACTIONr_mcangle_it3.2231291
X-RAY DIFFRACTIONr_scbond_it2.3422583
X-RAY DIFFRACTIONr_scangle_it3.2493516
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 (%)
2-2.0520.408420.2728490.27891797.165
2.052-2.1080.356530.2398110.24686599.884
2.108-2.1690.382440.2338090.2486498.727
2.169-2.2350.281360.2177870.22823100
2.235-2.3080.261430.2047800.20882499.879
2.308-2.3880.247380.2047340.207772100
2.388-2.4780.251380.2087210.21759100
2.478-2.5780.298340.2166930.2272999.726
2.578-2.6920.244350.2236730.224708100
2.692-2.8220.297290.2246480.227677100
2.822-2.9730.244300.2266240.227654100
2.973-3.1520.253300.2215790.223609100
3.152-3.3670.246210.2025510.204572100
3.367-3.6330.334290.1855190.191548100
3.633-3.9740.28240.1924720.196496100
3.974-4.4330.244260.1674360.172462100
4.433-5.10.236170.1634020.166419100
5.1-6.2020.349120.2483390.251351100
6.202-8.5890.317210.2462700.251291100
8.589-300.12870.2321850.227192100

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