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- PDB-6t9y: CARBOXYPEPTIDASE T WITH N-SULFAMOYL-L-LYSIN -

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Basic information

Entry
Database: PDB / ID: 6t9y
TitleCARBOXYPEPTIDASE T WITH N-SULFAMOYL-L-LYSIN
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 / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2~{S})-6-azanyl-2-(sulfamoylamino)hexanoic acid / Carboxypeptidase T
Similarity search - Component
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 Å
AuthorsTimofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
CitationJournal: To Be Published
Title: CARBOXYPEPTIDASE T WITH N-SULFAMOYL-L-LYSIN
Authors: Timofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
History
DepositionOct 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 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.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Oct 23, 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)37,0927
Polymers36,6411
Non-polymers4516
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-47 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.050, 158.050, 104.391
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-595-

HOH

21A-654-

HOH

31A-731-

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-7B0 / (2~{S})-6-azanyl-2-(sulfamoylamino)hexanoic acid


Mass: 225.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N3O4S
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 5.14 Å3/Da / Density % sol: 76.05 %
Crystal growTemperature: 273 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 PILATUS 2M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. obs: 58676 / % possible obs: 99.76 % / Redundancy: 6.88 % / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.115 / Net I/σ(I): 5.9161
Reflection shellResolution: 1.92→2.02 Å / Rmerge(I) obs: 0.37 / Num. unique obs: 8429 / Rrim(I) all: 0.401

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3qnv


Resolution: 1.92→28.89 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.555 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.072
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.161 2966 5.1 %RANDOM
Rwork0.1466 ---
obs0.1473 55688 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.65 Å2 / Biso mean: 13.621 Å2 / Biso min: 2.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.92→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 19 269 2869
Biso mean--29.53 24.38 -
Num. residues----323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132682
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172280
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.6553650
X-RAY DIFFRACTIONr_angle_other_deg1.5951.5755317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.365326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.64323.133150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83815415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9971513
X-RAY DIFFRACTIONr_chiral_restr0.1010.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023062
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02589
LS refinement shellResolution: 1.92→1.97 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.178 210 -
Rwork0.175 4059 -
obs--99.3 %

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