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- PDB-3e5h: Crystal Structure of Rab28 GTPase in the Active (GppNHp-bound) Form -

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Basic information

Entry
Database: PDB / ID: 3e5h
TitleCrystal Structure of Rab28 GTPase in the Active (GppNHp-bound) Form
ComponentsRas-related protein Rab-28
KeywordsSIGNALING PROTEIN / Rab GTPase / Cell membrane / GTP-binding / Lipoprotein / Membrane / Nucleotide-binding / Prenylation
Function / homology
Function and homology information


ciliary rootlet / endomembrane system / ciliary basal body / intracellular protein transport / GDP binding / GTPase activity / GTP binding / plasma membrane / 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 / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...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 / 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-28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.499 Å
AuthorsLee, S.H. / Baek, K. / Li, Y. / Dominguez, R.
CitationJournal: Febs Lett. / Year: 2008
Title: Large nucleotide-dependent conformational change in Rab28.
Authors: Lee, S.H. / Baek, K. / Dominguez, R.
History
DepositionAug 13, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionAug 26, 2008ID: 2HY4
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 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 1.3Aug 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.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.value / _struct_conn.pdbx_dist_value / _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_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

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Assembly

Deposited unit
A: Ras-related protein Rab-28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7125
Polymers19,9811
Non-polymers7314
Water3,693205
1
A: Ras-related protein Rab-28
hetero molecules

A: Ras-related protein Rab-28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,42310
Polymers39,9622
Non-polymers1,4618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4580 Å2
ΔGint-41 kcal/mol
Surface area16390 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.747, 79.747, 66.977
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-258-

HOH

21A-259-

HOH

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Components

#1: Protein Ras-related protein Rab-28 / Rab-26


Mass: 19980.971 Da / Num. of mol.: 1 / Fragment: Rab28 (UNP residues 11-184)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: rab28 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51157
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 100 mM NaCl, 100 mM potassium acetate, 5% glycerol, 20 mM HEPES, pH 7.50, 2mM MgCl2, vapor diffusion, hanging drop, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 35267 / Num. obs: 35232 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.2 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Χ2: 1.276 / Net I/σ(I): 47.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 10 / Num. unique all: 3453 / Rsym value: 0.321 / Χ2: 1.057 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
RefinementStarting model: PDB ENTRY 2HXS

2hxs


Resolution: 1.499→28.794 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.15 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1764 5.01 %RANDOM
Rwork0.151 ---
all0.153 35207 --
obs0.153 35175 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.288 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso max: 68.33 Å2 / Biso mean: 22.972 Å2 / Biso min: 9.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.346 Å2-0 Å20 Å2
2---0.346 Å2-0 Å2
3---0.692 Å2
Refinement stepCycle: LAST / Resolution: 1.499→28.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1396 0 45 205 1646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071617
X-RAY DIFFRACTIONf_angle_d1.2022224
X-RAY DIFFRACTIONf_chiral_restr0.076255
X-RAY DIFFRACTIONf_plane_restr0.004276
X-RAY DIFFRACTIONf_dihedral_angle_d17.825631
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.499-1.540.1791410.1225012642100
1.54-1.5850.1661300.10925222652100
1.585-1.6360.1531340.10825522686100
1.636-1.6950.1511260.10525292655100
1.695-1.7630.1481410.10725402681100
1.763-1.8430.1631430.11225172660100
1.843-1.940.1611250.1225612686100
1.94-2.0620.1651330.12225502683100
2.062-2.2210.1681270.13325952722100
2.221-2.4440.1431160.13825842700100
2.444-2.7970.2051630.16325782741100
2.797-3.5230.1811410.16226242765100
3.523-28.7990.1981440.1812758290299

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