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- PDB-4gn8: mouse SMP30/GNL-1,5-AG complex -

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Basic information

Entry
Database: PDB / ID: 4gn8
Titlemouse SMP30/GNL-1,5-AG complex
ComponentsRegucalcin
KeywordsHYDROLASE / beta propeller structure
Function / homology
Function and homology information


negative regulation of DNA catabolic process / negative regulation of RNA biosynthetic process / negative regulation of flagellated sperm motility / negative regulation of bone development / gluconolactonase / gluconolactonase activity / positive regulation of proteolysis involved in protein catabolic process / positive regulation of triglyceride biosynthetic process / negative regulation of nitric oxide biosynthetic process / positive regulation of fatty acid biosynthetic process ...negative regulation of DNA catabolic process / negative regulation of RNA biosynthetic process / negative regulation of flagellated sperm motility / negative regulation of bone development / gluconolactonase / gluconolactonase activity / positive regulation of proteolysis involved in protein catabolic process / positive regulation of triglyceride biosynthetic process / negative regulation of nitric oxide biosynthetic process / positive regulation of fatty acid biosynthetic process / L-ascorbic acid biosynthetic process / positive regulation of glucose metabolic process / negative regulation of DNA biosynthetic process / positive regulation of ATP-dependent activity / enzyme regulator activity / regulation of calcium-mediated signaling / negative regulation of protein phosphorylation / kidney development / liver regeneration / intracellular calcium ion homeostasis / negative regulation of epithelial cell proliferation / spermatogenesis / calcium ion binding / negative regulation of apoptotic process / 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
1,5-anhydro-D-glucitol / Regucalcin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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_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_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

Downloads & links

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Assembly

Deposited unit
A: Regucalcin
B: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,69226
Polymers66,8862
Non-polymers2,80624
Water8,467470
1
A: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3328
Polymers33,4431
Non-polymers8897
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,36018
Polymers33,4431
Non-polymers1,91817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.587, 102.587, 149.706
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Sugar
ChemComp-ASO / 1,5-anhydro-D-glucitol / 1,5-ANHYDROSORBITOL / 1,5-Anhydroglucitol


Type: D-saccharide / Mass: 164.156 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
D-1-deoxy-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 3.4 Å3/Da / Density % sol: 63.82 %
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: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→76.4 Å / Num. all: 100497 / Num. obs: 100497 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.15 Å2
Reflection shellResolution: 1.7→1.79 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: 4GN9

4gn9


Resolution: 1.7→49.902 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8884 / SU ML: 0.13 / σ(F): 1.99 / Phase error: 18.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 5024 5 %Random
Rwork0.1705 ---
all0.1714 100492 --
obs0.1714 100492 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.42 Å2 / Biso mean: 23.6405 Å2 / Biso min: 11.41 Å2
Refinement stepCycle: LAST / Resolution: 1.7→49.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4616 0 166 470 5252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074989
X-RAY DIFFRACTIONf_angle_d1.1666806
X-RAY DIFFRACTIONf_chiral_restr0.088764
X-RAY DIFFRACTIONf_plane_restr0.005865
X-RAY DIFFRACTIONf_dihedral_angle_d13.7071820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.71930.25211670.211731663333100
1.7193-1.73950.2371670.204931673334100
1.7395-1.76080.2411660.198731493315100
1.7608-1.78310.22481640.194231223286100
1.7831-1.80650.24081650.190531413306100
1.8065-1.83130.21111680.182531903358100
1.8313-1.85740.20921660.184731463312100
1.8574-1.88520.2131640.176531123276100
1.8852-1.91460.19651660.183431623328100
1.9146-1.9460.19821660.17931633329100
1.946-1.97960.23651670.185131723339100
1.9796-2.01560.20671670.179931733340100
2.0156-2.05430.2411660.17931463312100
2.0543-2.09630.20421670.170731763343100
2.0963-2.14180.19811660.169431473313100
2.1418-2.19170.19881670.177331853352100
2.1917-2.24650.18921670.172331583325100
2.2465-2.30720.21291660.178431633329100
2.3072-2.37510.20971660.173431803346100
2.3751-2.45180.20621680.173431893357100
2.4518-2.53940.18591680.180831773345100
2.5394-2.64110.22321680.182631913359100
2.6411-2.76120.20831660.183431723338100
2.7612-2.90680.19451690.182331953364100
2.9068-3.08890.19231690.185332103379100
3.0889-3.32740.18521680.168232083376100
3.3274-3.66210.16211700.149832303400100
3.6621-4.19180.14061710.135832413412100
4.1918-5.28030.12751720.131932763448100
5.2803-49.92350.21871770.20133361353898

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