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- PDB-4gnb: human SMP30/GNL -

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Basic information

Entry
Database: PDB / ID: 4gnb
Titlehuman 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 / 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 / positive regulation of glucose metabolic process / L-ascorbic acid biosynthetic 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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_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_auth_seq_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 / _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

Downloads & links

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Assembly

Deposited unit
A: Regucalcin
B: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7045
Polymers66,5842
Non-polymers1203
Water7,044391
1
A: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3322
Polymers33,2921
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3723
Polymers33,2921
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.500, 50.786, 86.563
Angle α, β, γ (deg.)90.00, 100.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33291.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMP30 / Plasmid: pET-21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta2 pLysS / References: UniProt: Q15493, gluconolactonase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% PEG6000, 100mM Tris-HCl, 5mM CaCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 87006 / Num. obs: 87006 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.31 Å2
Reflection shellResolution: 1.5→1.58 Å / % possible all: 96

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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: 3G4E

3g4e


Resolution: 1.5→19.531 Å / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.8568 / SU ML: 0.17 / σ(F): 1.99 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 4349 5 %Random
Rwork0.1893 ---
all0.1907 86999 --
obs0.1907 86999 98.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.2 Å2 / Biso mean: 16.7576 Å2 / Biso min: 4.55 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4564 0 3 391 4958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074722
X-RAY DIFFRACTIONf_angle_d1.1446423
X-RAY DIFFRACTIONf_chiral_restr0.079701
X-RAY DIFFRACTIONf_plane_restr0.006843
X-RAY DIFFRACTIONf_dihedral_angle_d13.3221709
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 (%)
1.5-1.5170.30081380.26492633277195
1.517-1.53490.33231410.25232678281996
1.5349-1.55360.2471400.23912655279596
1.5536-1.57330.26271430.23912717286096
1.5733-1.59390.29081420.23162691283397
1.5939-1.61580.26061420.22972709285198
1.6158-1.63880.27031440.2162723286797
1.6388-1.66330.24661420.21812706284898
1.6633-1.68930.26521450.21672754289998
1.6893-1.71690.26371430.21922708285198
1.7169-1.74650.26251470.21442792293998
1.7465-1.77830.27631420.2092700284298
1.7783-1.81250.27341450.20942765291099
1.8125-1.84940.29861460.20632767291399
1.8494-1.88960.24321450.20312760290599
1.8896-1.93350.25131460.19622762290899
1.9335-1.98180.22381450.1942758290399
1.9818-2.03540.1991470.18822794294199
2.0354-2.09520.20851470.18382799294699
2.0952-2.16270.20921460.17872772291899
2.1627-2.23990.20541470.185427812928100
2.2399-2.32950.21881460.179627852931100
2.3295-2.43530.21221460.184428002946100
2.4353-2.56340.21291490.187228152964100
2.5634-2.72360.2221470.195428032950100
2.7236-2.93330.24011480.186828162964100
2.9333-3.22730.20171490.189628192968100
3.2273-3.69150.18741480.167928162964100
3.6915-4.64060.16411480.1562818296699
4.6406-19.53220.19761450.18082754289994

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