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- PDB-3dlj: Crystal structure of human carnosine dipeptidase 1 -

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Basic information

Entry
Database: PDB / ID: 3dlj
TitleCrystal structure of human carnosine dipeptidase 1
ComponentsBeta-Ala-His dipeptidase
KeywordsHYDROLASE / CNDP1 / Carnosine dipeptidase 1 / Structural Genomics / Structural Genomics Consortium / SGC / metallopeptidase M20 family / Carboxypeptidase / Glycoprotein / Metal-binding / Metalloprotease / Protease / Secreted
Function / homology
Function and homology information


beta-Ala-His dipeptidase / regulation of protein metabolic process => GO:0051246 / metallodipeptidase activity / dipeptidase activity / carboxypeptidase activity / peptidase activity / proteolysis / extracellular region / 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 / Aminopeptidase ...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
Beta-Ala-His dipeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsDong, A. / Dobrovetsky, E. / Seitova, A. / He, H. / Tempel, W. / Kozieradzki, I. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Edwards, A.M. ...Dong, A. / Dobrovetsky, E. / Seitova, A. / He, H. / Tempel, W. / Kozieradzki, I. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Bochkarev, A. / Cossar, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human carnosine dipeptidase 1.
Authors: Dobrovetsky, E. / Dong, A. / Seitova, A. / He, H. / Tempel, W. / Kozieradzki, I. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Bochkarev, A. / Cossar, D.
History
DepositionJun 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: Beta-Ala-His dipeptidase
B: Beta-Ala-His dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,95322
Polymers108,5952
Non-polymers35820
Water3,837213
1
A: Beta-Ala-His dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,52513
Polymers54,2981
Non-polymers22712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-Ala-His dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4289
Polymers54,2981
Non-polymers1318
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-19.1 kcal/mol
Surface area33760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.106, 75.613, 103.716
Angle α, β, γ (deg.)90.00, 109.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-Ala-His dipeptidase / Carnosine dipeptidase 1 / CNDP dipeptidase 1 / Serum carnosinase / Glutamate carboxypeptidase-like protein 2


Mass: 54297.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNDP1, CN1, CPGL2 / Cell line (production host): sf9 insect cells / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96KN2, beta-Ala-His dipeptidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 15 / Source method: obtained synthetically
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 4000, 0.2M Ammonium sulfate, 0.1M Na Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.96749 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2008 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96749 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 51418 / Num. obs: 51418 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 42.7 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 11.6
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.401 / % possible all: 85.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MAR345CCDdata collection
DENZOdata reduction
SCALEPACKdata scaling
ARP/wARP6.1.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZOF

2zof


Resolution: 2.26→29.91 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 12.958 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25402 1051 2 %RANDOM
Rwork0.20002 ---
obs0.20109 50255 97.29 %-
all-50255 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.634 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20.09 Å2
2---0.28 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.26→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7183 0 24 213 7420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227350
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.95710000
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4515930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67624.423312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.691151169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2551533
X-RAY DIFFRACTIONr_chiral_restr0.090.21142
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025558
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.23206
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24960
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2338
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.10.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6481.54812
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09227506
X-RAY DIFFRACTIONr_scbond_it1.72732907
X-RAY DIFFRACTIONr_scangle_it2.6844.52494
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.26→2.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 70 -
Rwork0.275 3136 -
obs--83.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.90440.5596-0.8920.6513-0.71661.3442-0.0878-0.1114-0.1274-0.1474-0.06620.01650.2753-0.11210.154-0.0951-0.0031-0.0021-0.0416-0.0232-0.083425.0040.8829.097
20.8660.58510.36131.01020.77062.7526-0.0748-0.11750.1446-0.14850.02780.0006-0.40640.70660.047-0.117-0.0376-0.02150.03180.0182-0.120354.53735.27425.125
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 4808 - 484
2X-RAY DIFFRACTION2BB8 - 48012 - 484

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