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- PDB-2gao: Crystal Structure of Human SAR1a in Complex With GDP -

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Basic information

Entry
Database: PDB / ID: 2gao
TitleCrystal Structure of Human SAR1a in Complex With GDP
ComponentsGTP-binding protein SAR1a
KeywordsPROTEIN TRANSPORT / gtpase / structural genomics consortium / gdp / SGC
Function / homology
Function and homology information


regulation of COPII vesicle coating / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / intracellular protein transport / GTPase activity ...regulation of COPII vesicle coating / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / intracellular protein transport / GTPase activity / GTP binding / Golgi apparatus
Similarity search - Function
small GTPase SAR1 family profile. / Small GTPase superfamily, SAR1-type / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...small GTPase SAR1 family profile. / Small GTPase superfamily, SAR1-type / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / 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 / GTP-binding protein SAR1a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsWang, J. / Dimov, S. / Tempel, W. / 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 SAR1a in Complex With GDP
Authors: Wang, J. / Dimov, S. / Tempel, W. / Yaniw, D. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionMar 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300Author states that biological unit for the protein is not yet known

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding protein SAR1a
B: GTP-binding protein SAR1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3046
Polymers46,4172
Non-polymers8864
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.295, 63.814, 62.132
Angle α, β, γ (deg.)90.00, 105.94, 90.00
Int Tables number4
Space group name H-MP1211
Detailsnot known

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Components

#1: Protein GTP-binding protein SAR1a / COPII-associated small GTPase


Mass: 23208.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAR1A, SAR1, SARA, SARA1 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE-3)-RIL / References: UniProt: Q9NR31
#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.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30% PEG8000, 0.2M ammonium sulfate, 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 7, 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: 29052 / % possible obs: 99.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.199 / Χ2: 1.356 / Net I/σ(I): 5
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Num. unique obsΧ2Rmerge(I) obs
2-2.0799.2428751.096
2.07-2.151004.228831.3810.788
2.15-2.251004.229111.2380.627
2.25-2.371004.228691.1920.621
2.37-2.521004.328991.210.489
2.52-2.711004.329031.2190.406
2.71-2.991004.328981.2720.3
2.99-3.421004.429161.5440.16
3.42-4.311004.429081.7960.092
4.31-3099.54.329901.560.057

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Phasing

PhasingMethod: molecular replacement

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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: 1F6B

1f6b


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.228 / WRfactor Rwork: 0.191 / SU B: 5.341 / SU ML: 0.146 / ESU R: 0.188 / ESU R Free: 0.175
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, ARP/wARP by LAMZIN,PERRAKIS,MORRIS was also used for refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2694 1470 5.067 %thin shells
Rwork0.2238 ---
all0.226 ---
obs-29010 99.227 %-
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: 18.669 Å2
Baniso -1Baniso -2Baniso -3
1-0.914 Å20 Å20.138 Å2
2---1.376 Å20 Å2
3---0.538 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2661 0 58 61 2780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222764
X-RAY DIFFRACTIONr_bond_other_d0.0020.021861
X-RAY DIFFRACTIONr_angle_refined_deg1.4222.0073742
X-RAY DIFFRACTIONr_angle_other_deg0.95334560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9355334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11224.375112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56415508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7161514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022952
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02542
X-RAY DIFFRACTIONr_nbd_refined0.20.2491
X-RAY DIFFRACTIONr_nbd_other0.1870.21917
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21306
X-RAY DIFFRACTIONr_nbtor_other0.0820.21327
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0660.26
X-RAY DIFFRACTIONr_mcbond_it2.7122160
X-RAY DIFFRACTIONr_mcbond_other0.6052692
X-RAY DIFFRACTIONr_mcangle_it3.21732682
X-RAY DIFFRACTIONr_scbond_it2.21821301
X-RAY DIFFRACTIONr_scangle_it3.01931058
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 (%)
2-2.0520.39980.30618640.31214691.426
2.052-2.1080.336980.29319360.295203899.804
2.108-2.1690.355980.28319360.286203699.902
2.169-2.2350.344980.28118780.2841976100
2.235-2.3080.328980.27318210.276192399.792
2.308-2.3880.301980.2517840.2531882100
2.388-2.4780.29980.23616810.2391779100
2.478-2.5780.27980.23416160.236171699.883
2.578-2.6920.251980.2315620.2311660100
2.692-2.8220.258490.2315250.231157599.937
2.822-2.9730.268980.23714250.2391523100
2.973-3.1520.27490.22413560.226141099.645
3.152-3.3670.278980.20812530.2131351100
3.367-3.6330.236490.19112000.1931249100
3.633-3.9740.259490.18111120.184116599.657
3.974-4.4330.232490.16710020.17105399.81
4.433-5.10.162490.1688850.16893599.893
5.1-6.2020.236490.2087420.209791100
6.202-8.5890.227490.2215880.22163899.843
8.589-3000.2073740.20739095.897

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