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- PDB-4gn7: mouse SMP30/GNL -

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Basic information

Entry
Database: PDB / ID: 4gn7
Titlemouse SMP30/GNL
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 / gluconolactonase / negative regulation of bone development / 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 / gluconolactonase / negative regulation of bone development / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)68,21517
Polymers66,8862
Non-polymers1,32915
Water6,720373
1
A: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0598
Polymers33,4431
Non-polymers6167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1559
Polymers33,4431
Non-polymers7138
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.678, 102.678, 147.817
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 / 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.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 3.36 Å3/Da / Density % sol: 63.43 %
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: 1.95→76.2 Å / Num. all: 66230 / Num. obs: 66230 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 28.69 Å2
Reflection shellResolution: 1.95→2.06 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: 1.95→51.339 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8569 / SU ML: 0.18 / σ(F): 1.99 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 3311 5 %Random
Rwork0.1852 ---
all0.1867 66221 --
obs0.1867 66221 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.31 Å2 / Biso mean: 32.1372 Å2 / Biso min: 18.53 Å2
Refinement stepCycle: LAST / Resolution: 1.95→51.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4617 0 67 373 5057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074791
X-RAY DIFFRACTIONf_angle_d1.1696513
X-RAY DIFFRACTIONf_chiral_restr0.087705
X-RAY DIFFRACTIONf_plane_restr0.005840
X-RAY DIFFRACTIONf_dihedral_angle_d13.5261719
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9501-1.97790.27091390.224226362775100
1.9779-2.00740.26041350.214425672702100
2.0074-2.03880.24821350.21525642699100
2.0388-2.07220.25021370.198626132750100
2.0722-2.1080.24981360.202825742710100
2.108-2.14630.24211370.207526112748100
2.1463-2.18760.2481360.20225812717100
2.1876-2.23220.25431360.194725892725100
2.2322-2.28080.2311380.193626212759100
2.2808-2.33380.22181380.201426102748100
2.3338-2.39220.22541360.194125792715100
2.3922-2.45690.25751360.197325862722100
2.4569-2.52920.24791370.200926092746100
2.5292-2.61080.24831370.201126102747100
2.6108-2.70410.25961370.212926002737100
2.7041-2.81240.26261390.216926362775100
2.8124-2.94030.24841380.225226212759100
2.9403-3.09530.28181380.221626272765100
3.0953-3.28930.22491390.196826402779100
3.2893-3.54320.19781380.179626202758100
3.5432-3.89960.1911400.157926542794100
3.8996-4.46360.16611400.143126692809100
4.4636-5.62260.16561420.142827032845100
5.6226-51.35680.1821470.18792790293799

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