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- PDB-6f6q: Carboxypeptidase T mutant L254N with Sulphamoil Arginine -

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Basic information

Entry
Database: PDB / ID: 6f6q
TitleCarboxypeptidase T mutant L254N with Sulphamoil Arginine
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. / 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~2~-sulfamoyl-L-arginine / Carboxypeptidase T
Similarity search - Component
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.79 Å
AuthorsTimofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
CitationJournal: To Be Published
Title: Carboxypeptidase T mutant L254N with Sulphamoil Arginine
Authors: Timofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
History
DepositionDec 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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_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)37,44911
Polymers36,6421
Non-polymers80710
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-91 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.810, 157.810, 103.940
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-613-

HOH

21A-679-

HOH

31A-818-

HOH

41A-828-

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, 348 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-0X9 / N~2~-sulfamoyl-L-arginine


Type: L-peptide linking / Mass: 253.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N5O4S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 296 K / Method: liquid diffusion / Details: SA 1.4%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.85 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.79→29.82 Å / Num. obs: 71613 / % possible obs: 99.65 % / Redundancy: 30.63 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.5902
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 9.44 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 10121 / % possible all: 97.86

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.79→28.77 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.029 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.05 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13127 3626 5.1 %RANDOM
Rwork0.11527 ---
obs0.11608 67962 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.32 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.79→28.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 37 338 2956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022752
X-RAY DIFFRACTIONr_bond_other_d0.0020.022300
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.943756
X-RAY DIFFRACTIONr_angle_other_deg0.99835375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5335340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1124.388139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60915421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5751513
X-RAY DIFFRACTIONr_chiral_restr0.0860.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023156
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02596
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0241.5461336
X-RAY DIFFRACTIONr_mcbond_other1.0151.5431335
X-RAY DIFFRACTIONr_mcangle_it1.3032.3241684
X-RAY DIFFRACTIONr_mcangle_other1.3032.3281685
X-RAY DIFFRACTIONr_scbond_it1.61.7451414
X-RAY DIFFRACTIONr_scbond_other1.5871.7361411
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7672.5242066
X-RAY DIFFRACTIONr_long_range_B_refined2.38719.8053389
X-RAY DIFFRACTIONr_long_range_B_other2.10619.0773313
X-RAY DIFFRACTIONr_rigid_bond_restr2.1435049
X-RAY DIFFRACTIONr_sphericity_free21.5515228
X-RAY DIFFRACTIONr_sphericity_bonded6.13655094
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 222 -
Rwork0.157 4809 -
obs--96.23 %

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