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- PDB-6sn6: CARBOXYPEPTIDASE T WITH N-SULFAMOYL-L-GLUTAMIC ACID -

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Basic information

Entry
Database: PDB / ID: 6sn6
TitleCARBOXYPEPTIDASE T WITH N-SULFAMOYL-L-GLUTAMIC ACID
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
N-sulfamoyl-L-glutamic acid / Carboxypeptidase T
Similarity search - Component
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsTimofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
CitationJournal: To Be Published
Title: CARBOXYPEPTIDASE T WITH N-SULFAMOYL-L-GLUTAMIC ACID
Authors: Timofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
History
DepositionAug 23, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionOct 9, 2019ID: 5MYH
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)37,0536
Polymers36,6411
Non-polymers4125
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-37 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.730, 158.730, 105.670
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-613-

HOH

21A-670-

HOH

31A-819-

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-3K0 / N-sulfamoyl-L-glutamic acid


Mass: 226.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 5.24 Å3/Da / Density % sol: 76.54 %
Crystal growTemperature: 294 K / Method: counter-diffusion / Details: SA 1.4 M

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.93→30 Å / Num. obs: 58550 / % possible obs: 98.98 % / Redundancy: 31.59 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 14.75
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 15.13 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 6822 / % possible all: 94.49

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→27.93 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.799 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.067
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1449 2959 5.1 %RANDOM
Rwork0.1122 ---
obs0.1138 55566 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.49 Å2 / Biso mean: 17.73 Å2 / Biso min: 9.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0 Å2
2---0.04 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 1.93→27.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 18 322 2921
Biso mean--31.28 32.46 -
Num. residues----323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0132800
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172333
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.6543803
X-RAY DIFFRACTIONr_angle_other_deg1.611.5745457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2365350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03323.268153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88115429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8291513
X-RAY DIFFRACTIONr_chiral_restr0.10.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023247
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02612
X-RAY DIFFRACTIONr_rigid_bond_restr4.52735129
LS refinement shellResolution: 1.93→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.16 180 -
Rwork0.116 3738 -
all-3918 -
obs--91.61 %

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