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- PDB-4ruh: Crystal structure of Human Carnosinase-2 (CN2) in complex with in... -

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Basic information

Entry
Database: PDB / ID: 4ruh
TitleCrystal structure of Human Carnosinase-2 (CN2) in complex with inhibitor, Bestatin at 2.25 A
ComponentsCytosolic non-specific dipeptidase
KeywordsHYDROLASE / Structural Genomics / Enzyme Function Initiative / Carboxypeptidase / Metalloprotease / Protease / substrate carnosine(dipeptide) / cofactor Manganese / cytosolic
Function / homology
Function and homology information


cytosol nonspecific dipeptidase / : / Glutathione synthesis and recycling / metallodipeptidase activity / dipeptidase activity / Paracetamol ADME / carboxypeptidase activity / proteolysis / extracellular exosome / nucleoplasm ...cytosol nonspecific dipeptidase / : / Glutathione synthesis and recycling / metallodipeptidase activity / dipeptidase activity / Paracetamol ADME / carboxypeptidase activity / proteolysis / extracellular exosome / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
Cytosolic nonspecific dipeptidase/DUG1 / : / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases ...Cytosolic nonspecific dipeptidase/DUG1 / : / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BES / : / Cytosolic non-specific dipeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å
Authorspandya, V. / Kaushik, A. / Singh, A.K. / Singh, R.P. / Kumaran, S.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Human Carnosinase-2 (CN2) in complex with inhibitor, Bestatin at 2.25 A
Authors: pandya, V. / Kaushik, A. / Singh, A.K. / Singh, R.P. / Kumaran, S.
History
DepositionNov 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _struct_conn.ptnr2_label_asym_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: Cytosolic non-specific dipeptidase
B: Cytosolic non-specific dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,91310
Polymers105,8932
Non-polymers1,0218
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-43 kcal/mol
Surface area31570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.090, 100.070, 105.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsHomodimer

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Components

#1: Protein Cytosolic non-specific dipeptidase / CNDP dipeptidase 2 / Glutamate carboxypeptidase-like protein 1 / Peptidase A


Mass: 52946.312 Da / Num. of mol.: 2 / Fragment: Human carnosinase-2 (CN-2)
Source method: isolated from a genetically manipulated source
Details: longevity / Source: (gene. exp.) Homo sapiens (human)
Gene: CN2, CNDP dipeptidase 2 (metallopeptidase M20 family) [ Homo sapiens (human), CNDP2, CPGL, PEPA
Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q96KP4, cytosol nonspecific dipeptidase
#2: Chemical ChemComp-BES / 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID / BESTATIN


Mass: 308.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H24N2O4 / Comment: protease inhibitor*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 8
Details: 0.2M Hepes. 25% PPEG 4000, 100mm NaCl, pH 8.0, LIQUID DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97755 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 20, 2013 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97755 Å / Relative weight: 1
ReflectionResolution: 2.25→33.6 Å / % possible obs: 23 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.2
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 6.5 / Num. unique all: 6089

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementResolution: 2.25→33.6 Å / SU ML: 0.34 / σ(F): 1.31 / Phase error: 28.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2823 3769 5.03 %
Rwork0.2188 --
obs0.222 74921 88.43 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.578 Å2 / ksol: 0.416 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.0641 Å20 Å2-0 Å2
2--10.2099 Å2-0 Å2
3----4.1458 Å2
Refinement stepCycle: LAST / Resolution: 2.25→33.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7016 0 60 228 7304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117250
X-RAY DIFFRACTIONf_angle_d1.1639835
X-RAY DIFFRACTIONf_dihedral_angle_d14.7892631
X-RAY DIFFRACTIONf_chiral_restr0.0721074
X-RAY DIFFRACTIONf_plane_restr0.0051256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.27850.2971480.20722577X-RAY DIFFRACTION89
2.2785-2.30850.32221360.22952708X-RAY DIFFRACTION90
2.3085-2.34010.3241250.22922702X-RAY DIFFRACTION90
2.3401-2.37350.34741600.23222645X-RAY DIFFRACTION90
2.3735-2.40890.33131420.23452692X-RAY DIFFRACTION90
2.4089-2.44650.33411220.22942676X-RAY DIFFRACTION89
2.4465-2.48660.32091340.20762678X-RAY DIFFRACTION90
2.4866-2.52950.29341410.21292649X-RAY DIFFRACTION90
2.5295-2.57550.29011560.212676X-RAY DIFFRACTION89
2.5755-2.6250.33961400.21872618X-RAY DIFFRACTION89
2.625-2.67860.26421320.25632667X-RAY DIFFRACTION89
2.6786-2.73680.31641360.22892670X-RAY DIFFRACTION89
2.7368-2.80040.30191420.21992661X-RAY DIFFRACTION89
2.8004-2.87040.32221420.22562626X-RAY DIFFRACTION88
2.8704-2.9480.33121390.22632642X-RAY DIFFRACTION88
2.948-3.03470.26631300.2152640X-RAY DIFFRACTION88
3.0347-3.13250.27991650.20882603X-RAY DIFFRACTION89
3.1325-3.24440.30351240.21482654X-RAY DIFFRACTION88
3.2444-3.37420.3151550.21972588X-RAY DIFFRACTION88
3.3742-3.52760.28871380.21432630X-RAY DIFFRACTION88
3.5276-3.71340.23721120.2042630X-RAY DIFFRACTION87
3.7134-3.94570.27151570.20712593X-RAY DIFFRACTION88
3.9457-4.24980.20141510.20022578X-RAY DIFFRACTION87
4.2498-4.67650.22961550.18872581X-RAY DIFFRACTION87
4.6765-5.35080.25471190.20472604X-RAY DIFFRACTION87
5.3508-6.73260.23371510.25452589X-RAY DIFFRACTION87
6.7326-33.62740.27241170.26672575X-RAY DIFFRACTION86

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