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- PDB-3v7z: Carboxypeptidase T with GEMSA -

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Basic information

Entry
Database: PDB / ID: 3v7z
TitleCarboxypeptidase T with GEMSA
ComponentsCarboxypeptidase T
KeywordsHYDROLASE / Peptidase
Function / homology
Function and homology information


carboxypeptidase T / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Carboxypeptidase T / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2-GUANIDINOETHYLMERCAPTO)SUCCINIC ACID / Carboxypeptidase T
Similarity search - Component
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsKuznetsov, S.A. / Timofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
CitationJournal: Febs J. / Year: 2015
Title: Structural insights into the broad substrate specificity of carboxypeptidase T from Thermoactinomyces vulgaris.
Authors: Akparov, V.K.h. / Timofeev, V.I. / Khaliullin, I.G. / Svedas, V. / Chestukhina, G.G. / Kuranova, I.P.
History
DepositionDec 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal_grow / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal_grow.method / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _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: Carboxypeptidase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,47730
Polymers36,9591
Non-polymers2,51829
Water6,107339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carboxypeptidase T
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)236,860180
Polymers221,7526
Non-polymers15,108174
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_545x,x-y-1,-z+1/21
Buried area50730 Å2
ΔGint-807 kcal/mol
Surface area58020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.890, 157.890, 104.195
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-600-

HOH

21A-823-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carboxypeptidase T


Mass: 36958.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Gene: cpt / Production host: Escherichia coli (E. coli) / References: UniProt: P29068, carboxypeptidase T

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Non-polymers , 7 types, 368 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GEM / (2-GUANIDINOETHYLMERCAPTO)SUCCINIC ACID / 2-GUANIDINOETHYLTHIO)SUCCINIC ACID / GUANIDINOETHYL MERCAPTOSUCCINIC ACID / GEMSA


Mass: 235.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N3O4S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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

Crystal growTemperature: 273 K / Method: counter-diffusion / Details: Counter diffusion, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorDetector: CCD / Date: Oct 9, 2011 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.61→10 Å / Num. obs: 93599 / % possible obs: 99.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→10 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.618 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.15211 4917 5 %RANDOM
Rwork0.13295 ---
obs0.13389 93599 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.61→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 151 339 3071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022968
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.131.9724026
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0625364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.56124.514144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28415450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4031514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212313
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr1.12932967
X-RAY DIFFRACTIONr_sphericity_free20.849592
X-RAY DIFFRACTIONr_sphericity_bonded8.93153158
LS refinement shellResolution: 1.61→1.651 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 348 -
Rwork0.203 6205 -
obs--99.56 %

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