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- PDB-2fa9: The crystal structure of Sar1[H79G]-GDP provides insight into the... -

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Basic information

Entry
Database: PDB / ID: 2fa9
TitleThe crystal structure of Sar1[H79G]-GDP provides insight into the coat-controlled GTP hydrolysis in the disassembly of COP II
ComponentsGTP-binding protein SAR1b
KeywordsPROTEIN TRANSPORT / Sar1H79G mutant
Function / homology
Function and homology information


regulation of lipid transport / lipoprotein transport / Golgi cisterna membrane / lipid homeostasis / vesicle-mediated transport / intracellular protein transport / GTPase activity / GTP binding / endoplasmic reticulum membrane / metal ion binding
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 SAR1b
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRao, Y. / Huang, M. / Yuan, C. / Bian, C. / Hou, X.
CitationJournal: Chin.J.Struct.Chem. / Year: 2006
Title: Crystal Structure of Sar1[H79G]-GDP Which Provides Insight into the Coat-controlled GTP Hydrolysis in the Disassembly of COP II
Authors: Rao, Y. / Yuan, C. / Bian, C. / Hou, X. / Li, Y. / Zhao, G. / Ye, X. / Huang, Z. / Huang, M.
History
DepositionDec 7, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 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.name
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP-binding protein SAR1b
B: GTP-binding protein SAR1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4308
Polymers42,3032
Non-polymers1,1276
Water2,180121
1
A: GTP-binding protein SAR1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7154
Polymers21,1511
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein SAR1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7154
Polymers21,1511
Non-polymers5643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.215, 61.620, 71.165
Angle α, β, γ (deg.)90.00, 72.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GTP-binding protein SAR1b / Sar1 / GTBPB


Mass: 21151.354 Da / Num. of mol.: 2 / Fragment: residues 10-198 / Mutation: H79G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Plasmid: pET11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9QVY3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 298 K / Method: evaporation, recrystallization / pH: 5.8
Details: 28%(w/v)Polyethylene Glycol-4000, 100mM sodium acetate, 0.2M ammonium sulfate , pH 5.8, EVAPORATION, RECRYSTALLIZATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54 Å
DetectorType: ENRAF-NONIUS / Detector: CCD / Date: Aug 11, 2005
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→46 Å / Num. all: 15488 / Num. obs: 13619 / % possible obs: 88.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.13 / Biso Wilson estimate: 21 Å2
Reflection shellHighest resolution: 2.5 Å / % possible all: 88.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
PROTEUM PLUSdata reduction
LSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F6B

1f6b


Resolution: 2.5→45.65 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1038337.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 824 6.1 %RANDOM
Rwork0.218 ---
obs0.218 13619 88.4 %-
all-15488 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.6333 Å2 / ksol: 0.368936 e/Å3
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1-9.99 Å20 Å2-2.62 Å2
2---9.66 Å20 Å2
3----0.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 68 121 2925
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it2.051.5
X-RAY DIFFRACTIONc_mcangle_it3.272
X-RAY DIFFRACTIONc_scbond_it3.22
X-RAY DIFFRACTIONc_scangle_it4.292.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 114 6.2 %
Rwork0.289 1721 -
obs--72.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2h79ggdp_xplor_par.txt
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ion.param

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