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- PDB-4gn9: mouse SMP30/GNL-glucose complex -

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Basic information

Entry
Database: PDB / ID: 4gn9
Titlemouse SMP30/GNL-glucose complex
ComponentsRegucalcin
KeywordsHYDROLASE / beta propeller structure
Function / homology
Function and homology information


gluconolactonase / gluconolactonase activity / L-ascorbic acid biosynthetic process / positive regulation of ATP-dependent activity / enzyme regulator activity / regulation of calcium-mediated signaling / intracellular calcium ion homeostasis / calcium ion binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Regucalcin / Senescence marker protein-30 (SMP-30) / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Regucalcin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAizawa, S. / Senda, M. / Harada, A. / Maruyama, N. / Ishida, T. / Aigaki, T. / Ishigami, A. / Senda, T.
CitationJournal: Plos One / Year: 2013
Title: Structural basis of the gamma-lactone-ring formation in ascorbic acid biosynthesis by the senescence marker protein-30/gluconolactonase
Authors: Aizawa, S. / Senda, M. / Harada, A. / Maruyama, N. / Ishida, T. / Aigaki, T. / Ishigami, A. / Senda, T.
History
DepositionAug 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regucalcin
B: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,98318
Polymers66,8862
Non-polymers2,09816
Water6,017334
1
A: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2157
Polymers33,4431
Non-polymers7736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,76811
Polymers33,4431
Non-polymers1,32510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.863, 101.863, 146.826
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Regucalcin / SMP30 / GNL / RC / Gluconolactonase / GNL / Senescence marker protein 30


Mass: 33442.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smp30 / Plasmid: pET-21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q64374, gluconolactonase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.6M ammonium sulfate, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 22, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→75.62 Å / Num. all: 60058 / Num. obs: 60058 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 26.62 Å2
Reflection shellResolution: 2→2.11 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GNB

4gnb


Resolution: 2→75.617 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8647 / SU ML: 0.19 / σ(F): 1.99 / Phase error: 20.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 3002 5 %Random
Rwork0.1759 ---
all0.1775 60052 --
obs0.1775 60052 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.36 Å2 / Biso mean: 32.0091 Å2 / Biso min: 16.49 Å2
Refinement stepCycle: LAST / Resolution: 2→75.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4614 0 128 334 5076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144918
X-RAY DIFFRACTIONf_angle_d1.2286710
X-RAY DIFFRACTIONf_chiral_restr0.085756
X-RAY DIFFRACTIONf_plane_restr0.005853
X-RAY DIFFRACTIONf_dihedral_angle_d14.3191793
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.03280.25171420.225127072849100
2.0328-2.06790.26111400.211626562796100
2.0679-2.10550.2521420.208926952837100
2.1055-2.1460.24891420.196426952837100
2.146-2.18980.26721400.212526672807100
2.1898-2.23740.23041410.201326852826100
2.2374-2.28950.2391430.204527042847100
2.2895-2.34670.23751410.200826852826100
2.3467-2.41020.24621420.199827062848100
2.4102-2.48110.26541420.202726872829100
2.4811-2.56120.25151400.203626712811100
2.5612-2.65270.25051430.194727022845100
2.6527-2.75890.24221440.227402884100
2.7589-2.88450.21921420.200527032845100
2.8845-3.03660.21921430.195827242867100
3.0366-3.22680.20761430.183926992842100
3.2268-3.4760.20721430.169427242867100
3.476-3.82580.16211460.155327682914100
3.8258-4.37930.1531450.132827542899100
4.3793-5.51720.16961460.133227902936100
5.5172-75.67130.19591520.17462888304099

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