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- PDB-6z28: Carboxypeptidase T mutant L254N with N-sulfamoyl-L-glutamic acid -

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Basic information

Entry
Database: PDB / ID: 6z28
TitleCarboxypeptidase T mutant L254N with N-sulfamoyl-L-glutamic acid
ComponentsCarboxypeptidase T
KeywordsHYDROLASE
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: 2.3 Å
AuthorsTimofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
CitationJournal: To Be Published
Title: CARBOXYPEPTIDASE T MUTANT L254N WITH WITH N-SULFAMOYL-L-GLUT
Authors: Timofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
History
DepositionMay 15, 2020Deposition site: PDBE / Processing site: PDBE
SupersessionMay 27, 2020ID: 6Q4L
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Derived calculations / Category: database_2 / 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.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 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

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Assembly

Deposited unit
A: Carboxypeptidase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2869
Polymers36,6421
Non-polymers6448
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-70 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.520, 158.520, 104.871
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-589-

HOH

21A-668-

HOH

31A-723-

HOH

41A-737-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carboxypeptidase T


Mass: 36642.223 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 , 5 types, 263 molecules

#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
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 293 K / Method: counter-diffusion / Details: 1.4 SA

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 34712 / % possible obs: 99.34 % / Redundancy: 10.61 % / Rmerge(I) obs: 0.228 / Rpim(I) all: 0.238 / Net I/σ(I): 2.4107
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3021 / Rpim(I) all: 0.384 / % possible all: 96.22

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QNV

3qnv


Resolution: 2.3→29.96 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.674 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 1742 5 %RANDOM
Rwork0.1581 ---
obs0.1596 32923 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.26 Å2 / Biso mean: 17.962 Å2 / Biso min: 8.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 2.3→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 29 255 2865
Biso mean--39.84 26.64 -
Num. residues----323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132741
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172281
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.6563703
X-RAY DIFFRACTIONr_angle_other_deg1.4931.5745323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7415332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.63423.179151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79515417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1661513
X-RAY DIFFRACTIONr_chiral_restr0.0910.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02594
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 125 -
Rwork0.215 2191 -
all-2316 -
obs--91.98 %

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