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- PDB-1f6b: CRYSTAL STRUCTURE OF SAR1-GDP COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1f6b
TitleCRYSTAL STRUCTURE OF SAR1-GDP COMPLEX
ComponentsSAR1COPII
KeywordsPROTEIN TRANSPORT / GTPASES / N-TERMINAL HELIX / MG-CONTAINING COMPLEX
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 / endoplasmic reticulum membrane / GTP binding / 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 / SYNCHROTRON / Resolution: 1.7 Å
AuthorsHuang, M. / Wilson, I.A. / Balch, W.E.
CitationJournal: J.Cell Biol. / Year: 2001
Title: Crystal structure of Sar1-GDP at 1.7 A resolution and the role of the NH2 terminus in ER export.
Authors: Huang, M. / Weissman, J.T. / Beraud-Dufour, S. / Luan, P. / Wang, C. / Chen, W. / Aridor, M. / Wilson, I.A. / Balch, W.E.
History
DepositionJun 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 99 The missing residues in remark 465 are either in N-terminal or are part of flexible switch regions ... The missing residues in remark 465 are either in N-terminal or are part of flexible switch regions (switch I: 48-59; switch II: 77-94

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAR1
B: SAR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,28711
Polymers44,8722
Non-polymers1,4159
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.368, 61.689, 71.142
Angle α, β, γ (deg.)90.00, 107.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SAR1 / COPII


Mass: 22435.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Plasmid: PET11D / Production host: Escherichia coli (E. coli) / 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.: 5 / 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.: 297 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG 4000, 0.2 M ammonium sulfate, and 0.1 M sodium acetate at pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11731
21731
31
41
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL7-111.08
SYNCHROTRONSSRL BL7-121.08
SYNCHROTRONSSRL BL9-230.9796
SYNCHROTRONSSRL BL9-240.9795
Detector
IDDetectorDate
1IMAGE PLATEFeb 13, 1999
2IMAGE PLATEJun 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.081
20.97961
30.97951
ReflectionResolution: 1.7→48 Å / Num. all: 48000 / Num. obs: 48000 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.26 / Num. unique all: 4269 / % possible all: 88.8
Reflection
*PLUS
Lowest resolution: 48 Å / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Lowest resolution: 1.81 Å / Mean I/σ(I) obs: 5.4

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Processing

Software
NameVersionClassification
PHASESphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→48.27 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 655230.09 / 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
Rfree0.24 1858 4 %RANDOM
Rwork0.22 ---
all0.22 48516 --
obs0.22 46658 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.49 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.7 Å20 Å20.54 Å2
2---2.51 Å20 Å2
3----1.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.7→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 83 297 3190
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d3.1
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it1.12
X-RAY DIFFRACTIONc_scangle_it1.682.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 244 3.5 %
Rwork0.251 6724 -
obs--86.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SAR.PAR
X-RAY DIFFRACTION3CARBOHYDRATE.PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM
X-RAY DIFFRACTION5ION.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / Num. reflection obs: 46597 / σ(F): 0 / Num. reflection Rfree: 1857 / % reflection Rfree: 4 % / Rfactor all: 0.22 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.1
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_scbond_it1.12
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scangle_it1.682.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.28 / % reflection Rfree: 3.5 % / Rfactor Rwork: 0.251 / Rfactor obs: 0.26

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