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- PDB-6tnk: CARBOXYPEPTIDASE T WITH N-SULFAMOYL-L-VALINE -

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Basic information

Entry
Database: PDB / ID: 6tnk
TitleCARBOXYPEPTIDASE T WITH N-SULFAMOYL-L-VALINE
ComponentsCarboxypeptidase T
KeywordsHYDROLASE / carboxypeptidase
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~{S})-3-methyl-2-(sulfamoylamino)butanoic acid / Carboxypeptidase T
Similarity search - Component
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTimofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
CitationJournal: To Be Published
Title: CARBOXYPEPTIDASE T WITH N-SULFAMOYL-L-VALINE
Authors: Timofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
History
DepositionDec 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)37,1038
Polymers36,6411
Non-polymers4627
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-59 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.531, 157.531, 104.523
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-623-

HOH

21A-671-

HOH

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Components

#1: Protein Carboxypeptidase T


Mass: 36641.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Gene: cpt / Production host: Thermoactinomyces vulgaris (bacteria) / References: UniProt: P29068, carboxypeptidase T
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NO5 / (2~{S})-3-methyl-2-(sulfamoylamino)butanoic acid


Mass: 196.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O4S
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

CrystalDensity Matthews: 5.11 Å3/Da / Density % sol: 75.92 %
Crystal growTemperature: 293 K / Method: counter-diffusion / Details: 1.4 SA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.9→29.98 Å / Num. obs: 60407 / % possible obs: 99.97 % / Redundancy: 17.49 % / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.148 / Net I/av σ(I): 3.8533 / Net I/σ(I): 15.1556
Reflection shellResolution: 1.9→2 Å / Redundancy: 18.25 % / Rmerge(I) obs: 0.33 / Num. unique obs: 8678 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QNV

3qnv


Resolution: 1.9→19.99 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.295 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.068
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1557 3001 5 %RANDOM
Rwork0.1423 ---
obs0.143 57327 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.46 Å2 / Biso mean: 13.757 Å2 / Biso min: 7.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.9→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 18 262 2861
Biso mean--13.99 24.52 -
Num. residues----323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132691
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172283
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.6593666
X-RAY DIFFRACTIONr_angle_other_deg1.6181.585327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3785330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.52723.087149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6215417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8451513
X-RAY DIFFRACTIONr_chiral_restr0.1310.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02593
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.168 193 -
Rwork0.151 4173 -
all-4366 -
obs--99.98 %

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