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- PDB-1gv9: p58/ERGIC-53 -

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Basic information

Entry
Database: PDB / ID: 1gv9
Titlep58/ERGIC-53
ComponentsP58/ERGIC-53
KeywordsCARBOHYDRATE BINDING / LECTIN
Function / homology
Function and homology information


postsynaptic Golgi apparatus / RHOD GTPase cycle / RAC2 GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / Cargo concentration in the ER / positive regulation of organelle organization / COPII-mediated vesicle transport / endoplasmic reticulum organization / COPII-coated ER to Golgi transport vesicle ...postsynaptic Golgi apparatus / RHOD GTPase cycle / RAC2 GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / Cargo concentration in the ER / positive regulation of organelle organization / COPII-mediated vesicle transport / endoplasmic reticulum organization / COPII-coated ER to Golgi transport vesicle / Golgi organization / endoplasmic reticulum-Golgi intermediate compartment / D-mannose binding / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / sarcomere / protein transport / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / glutamatergic synapse / endoplasmic reticulum / Golgi apparatus / metal ion binding / identical protein binding
Similarity search - Function
Legume-like lectin / : / Legume-like lectin family / L-type lectin-like (leguminous) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.46 Å
AuthorsVelloso, L.M. / Svensson, K. / Schneider, G. / Pettersson, R.F. / Lindqvist, Y.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of the Carbohydrate Recognition Domain of P58/Ergic-53, a Protein Involved in Glycoprotein Export from the Endoplasmic Reticulum.
Authors: Velloso, L.M. / Svensson, K. / Schneider, G. / Pettersson, R.F. / Lindqvist, Y.
History
DepositionFeb 7, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P58/ERGIC-53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4933
Polymers28,3011
Non-polymers1922
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.043, 85.407, 127.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein P58/ERGIC-53


Mass: 28301.328 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE RECOGNITION DOMAIN / Source method: isolated from a natural source / Source: (natural) RATTUS NORVEGICUS (Norway rat) / References: UniProt: Q62902
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.25 / Details: pH 7.25
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
31 mM1dropCaCl2
4100 mMsodium HEPES1reservoirpH7.25
51.6 M1reservoirLi2SO4
610 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.5418
DetectorType: MARRESEARCH
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.46→25 Å / Num. obs: 44706 / % possible obs: 95.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 22.2
Reflection shell
*PLUS
Highest resolution: 1.46 Å / Lowest resolution: 1.51 Å / % possible obs: 84.6 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 7.3

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.46→23.64 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.402 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2195 4.9 %RANDOM
Rwork0.191 ---
obs0.192 42377 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 1.46→23.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 10 191 1941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211810
X-RAY DIFFRACTIONr_bond_other_d0.0010.021537
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.4941.9142458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.67633576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022055
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02394
X-RAY DIFFRACTIONr_nbd_refined0.2390.3314
X-RAY DIFFRACTIONr_nbd_other0.2140.31480
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.5212
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1020.52
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.9420.328
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4590.344
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8041.51103
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51821769
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.893707
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0864.5689
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.46→1.5 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.222 147
Rwork0.199 2870
Refinement TLS params.Method: refined / Origin x: 0.0485 Å / Origin y: 23.6307 Å / Origin z: 18.2731 Å
111213212223313233
T0.007 Å20.003 Å2-0.0008 Å2-0.0099 Å20.0073 Å2--0.0068 Å2
L0.3039 °2-0.022 °2-0.0392 °2-0.3021 °20.007 °2--0.1625 °2
S0.0088 Å °0.0032 Å °-0.0201 Å °-0.037 Å °-0.0263 Å °0.0064 Å °0.0087 Å °0.0116 Å °0.0175 Å °
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor obs: 0.191 / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.49

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