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- PDB-3g4h: Crystal structure of Human Senescence Marker Protein-30 (Zinc Bound) -

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Basic information

Entry
Database: PDB / ID: 3g4h
TitleCrystal structure of Human Senescence Marker Protein-30 (Zinc Bound)
ComponentsRegucalcin
KeywordsHYDROLASE / six bladed beta propeller / gluconolactonase / organophosphate hydrolase / Regucalcin / Zinc bound / Alternative splicing / Calcium / Cytoplasm / Phosphoprotein / SIGNALING PROTEIN
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 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 1.2Sep 6, 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_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
B: Regucalcin
A: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2784
Polymers66,1472
Non-polymers1312
Water2,594144
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)33,1392
Polymers33,0731
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Regucalcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1392
Polymers33,0731
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.365, 52.019, 85.832
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
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 298 K / pH: 7.8
Details: 38% PEG 6000, 0.1M Tris-Hcl, 5mM DTT, 5mM CaCl2, 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
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 16, 2007
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: 1.92→84.52 Å / Num. obs: 42805 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 5.251
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.013 / Mean I/σ(I) obs: 0.5 / Rsym value: 0.01286 / % possible all: 94

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 37.74 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å26.01 Å
Translation2.5 Å26.01 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G4E

3g4e


Resolution: 1.92→84.52 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 1 / SU B: 13.655 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25336 2108 4.9 %RANDOM
Rwork0.22372 ---
obs0.22519 40630 99.23 %-
all-42738 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.462 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å21.66 Å2
2--1.08 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 1.92→84.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4606 0 2 144 4752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0224706
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5821.9546370
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.385592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28724.151212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.16615788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2391528
X-RAY DIFFRACTIONr_chiral_restr0.1840.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023594
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2610.22166
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23027
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2871.53085
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.36224720
X-RAY DIFFRACTIONr_scbond_it5.52531978
X-RAY DIFFRACTIONr_scangle_it7.2444.51650
X-RAY DIFFRACTIONr_rigid_bond_restr4.49735063
X-RAY DIFFRACTIONr_sphericity_free26.8753146
X-RAY DIFFRACTIONr_sphericity_bonded24.46934606
LS refinement shellResolution: 1.919→1.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 149 -
Rwork0.35 2784 -
obs--93.08 %

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