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- PDB-3prt: Mutant of the Carboxypeptidase T -

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Basic information

Entry
Database: PDB / ID: 3prt
TitleMutant of the Carboxypeptidase T
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. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsTimofeev, V.I. / Akparov, V.K. / Grishin, A.M. / Kuranova, I.P.
History
DepositionNov 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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_ref_seq_dif / 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_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_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

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Assembly

Deposited unit
A: Carboxypeptidase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,83417
Polymers36,5831
Non-polymers1,25116
Water4,216234
1


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

A: Carboxypeptidase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,66834
Polymers73,1662
Non-polymers2,50132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area6600 Å2
ΔGint-282 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.600, 157.600, 103.925
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-373-

HOH

21A-448-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carboxypeptidase T /


Mass: 36583.203 Da / Num. of mol.: 1 / Fragment: UNP Residues 99-421 / Mutation: G313S, A349G, T355A, D358G, T360D
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 , 5 types, 250 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 5.09 Å3/Da / Density % sol: 75.8 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.66→20 Å / Num. obs: 61748

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Processing

SoftwareName: REFMAC / Version: 5.5.0102 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OBR

1obr


Resolution: 1.66→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.173 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18756 3197 5 %RANDOM
Rwork0.16849 ---
obs0.16945 60746 71.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å2-0.53 Å20 Å2
2---1.07 Å20 Å2
3---1.6 Å2
Refinement stepCycle: LAST / Resolution: 1.66→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2577 0 68 234 2879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222807
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.9493823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9555347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.08724.348138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87115428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5961513
X-RAY DIFFRACTIONr_chiral_restr0.0780.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212204
X-RAY DIFFRACTIONr_mcbond_it0.6151.51681
X-RAY DIFFRACTIONr_mcangle_it1.14422737
X-RAY DIFFRACTIONr_scbond_it1.80631126
X-RAY DIFFRACTIONr_scangle_it2.8814.51086
X-RAY DIFFRACTIONr_rigid_bond_restr0.88932807
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 192 -
Rwork0.345 3942 -
obs--63.85 %

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