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- PDB-3g4e: Crystal structure of human senescence marker protein-30(SMP30)(Ca... -

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Basic information

Entry
Database: PDB / ID: 3g4e
TitleCrystal structure of human senescence marker protein-30(SMP30)(Calcium bound)
ComponentsRegucalcin
KeywordsHYDROLASE / six bladed beta-propeller / gluconolcatonase / organophosphate hydrolase / regucalcin / calcium bound / Alternative splicing / Calcium / Cytoplasm / Phosphoprotein
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsChakraborti, S. / Bahnson, B.J.
CitationJournal: Biochemistry / Year: 2010
Title: Crystal structure of human senescence marker protein 30: insights linking structural, enzymatic, and physiological functions .
Authors: Chakraborti, S. / Bahnson, B.J.
History
DepositionFeb 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_conn.ptnr2_label_seq_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)66,2274
Polymers66,1472
Non-polymers802
Water8,953497
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1142
Polymers33,0731
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1142
Polymers33,0731
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.474, 51.001, 86.124
Angle α, β, γ (deg.)90.00, 100.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Regucalcin / / RC / Senescence marker protein 30 / SMP-30


Mass: 33073.488 Da / Num. of mol.: 2 / Fragment: UNP residues 3-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGN, SMP30 / Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL codon plus / References: UniProt: Q15493
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 38% PEG 6000, 0.1M Tris-Hcl, 5mM calcium chloride, 5mM DTT, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 4, 2008
RadiationMonochromator: KOHZU HLD-4 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.41→84.819 Å / Num. obs: 14159 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 7.056
Reflection shellResolution: 1.41→1.49 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 0.8 / Num. measured all: 89400 / Num. unique all: 14159 / Rsym value: 0.808 / % possible all: 91.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.5 Å18.4 Å
Translation1.5 Å18.4 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
PHASERphasing
SHELXrefinement
PDB_EXTRACT3.006data extraction
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GHS

2ghs


Resolution: 1.42→8 Å / Num. parameters: 46695 / Num. restraintsaints: 57483 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.191 5201 5.3 %RANDOM
Rwork0.129 ---
obs0.136 14159 95.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso max: 157.09 Å2 / Biso mean: 25.472 Å2 / Biso min: 9.19 Å2
Refinement stepCycle: LAST / Resolution: 1.42→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4640 0 2 497 5139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0.061
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.072
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.038
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.059
X-RAY DIFFRACTIONs_approx_iso_adps0.094

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