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- PDB-4gna: mouse SMP30/GNL-xylitol complex -

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Basic information

Entry
Database: PDB / ID: 4gna
Titlemouse SMP30/GNL-xylitol 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 / gluconolactonase / gluconolactonase activity / L-ascorbic acid biosynthetic process / negative regulation of DNA biosynthetic process / negative regulation of bone development / : / positive regulation of triglyceride biosynthetic process ...negative regulation of DNA catabolic process / negative regulation of RNA biosynthetic process / negative regulation of flagellated sperm motility / gluconolactonase / gluconolactonase activity / L-ascorbic acid biosynthetic process / negative regulation of DNA biosynthetic process / negative regulation of bone development / : / positive regulation of triglyceride biosynthetic process / positive regulation of glucose metabolic process / positive regulation of fatty acid biosynthetic process / negative regulation of nitric oxide biosynthetic process / positive regulation of ATP-dependent activity / enzyme regulator activity / regulation of calcium-mediated signaling / negative regulation of epithelial cell proliferation / intracellular calcium ion homeostasis / 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
Xylitol / Regucalcin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / 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_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_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)67,71010
Polymers66,8862
Non-polymers8258
Water7,260403
1
A: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7314
Polymers33,4431
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9796
Polymers33,4431
Non-polymers5365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.967, 101.967, 147.548
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.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-XYL / Xylitol / D-Xylitol


Type: D-saccharide / Mass: 152.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H12O5
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 3.31 Å3/Da / Density % sol: 62.85 %
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: May 23, 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: 1.85→56.62 Å / Num. all: 76106 / Num. obs: 76106 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.66 Å2
Reflection shellResolution: 1.85→1.95 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: 1.85→56.616 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8845 / SU ML: 0.15 / σ(F): 1.99 / Phase error: 18.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1845 3805 5 %Random
Rwork0.1657 ---
all0.1667 76106 --
obs0.1667 76106 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.96 Å2 / Biso mean: 27.5923 Å2 / Biso min: 14.61 Å2
Refinement stepCycle: LAST / Resolution: 1.85→56.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 46 403 5079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064831
X-RAY DIFFRACTIONf_angle_d1.1416566
X-RAY DIFFRACTIONf_chiral_restr0.084717
X-RAY DIFFRACTIONf_plane_restr0.005853
X-RAY DIFFRACTIONf_dihedral_angle_d13.7861754
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.87340.26581380.217826202758100
1.8734-1.89810.26561390.204426472786100
1.8981-1.92410.22771400.196426672807100
1.9241-1.95160.21981400.189826472787100
1.9516-1.98070.22241380.188926402778100
1.9807-2.01170.21491390.188226552794100
2.0117-2.04470.20841400.178826502790100
2.0447-2.07990.20411400.172226602800100
2.0799-2.11770.22041390.171926432782100
2.1177-2.15850.23711400.172526632803100
2.1585-2.20250.21181400.174326512791100
2.2025-2.25040.18651390.175326522791100
2.2504-2.30280.21251410.178426682809100
2.3028-2.36040.20331410.174326872828100
2.3604-2.42420.21461410.177726812822100
2.4242-2.49550.19241410.178326642805100
2.4955-2.57610.23351380.179326362774100
2.5761-2.66810.21851410.179726782819100
2.6681-2.7750.23641420.177426862828100
2.775-2.90130.1861420.180726932835100
2.9013-3.05420.20971400.175126752815100
3.0542-3.24550.15221430.166327072850100
3.2455-3.49610.19431420.156227042846100
3.4961-3.84790.15771430.143427052848100
3.8479-4.40450.1461440.13727502894100
4.4045-5.54840.13261450.133827472892100
5.5484-56.64270.16731490.18462825297498

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