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- PDB-6go2: Carboxypeptidase T with N-sulfamoyl-L-Leucine -

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Basic information

Entry
Database: PDB / ID: 6go2
TitleCarboxypeptidase T with N-sulfamoyl-L-Leucine
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
Sulphamoil Leucine / 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-Leucine
Authors: Timofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
History
DepositionJun 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)37,1738
Polymers36,6411
Non-polymers5327
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-60 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.810, 157.810, 104.800
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-602-

HOH

21A-651-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 266 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.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-LU0 / Sulphamoil Leucine


Mass: 210.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2O4S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 293 K / Method: liquid diffusion / Details: 1.4 SA

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Data collection

DiffractionMean temperature: 100 K
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: 1.9→30 Å / Num. obs: 60665 / % possible obs: 99.86 % / Redundancy: 8.44 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 3.0774
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.55 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 8730 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QNV

3qnv


Resolution: 1.9→29.82 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.077 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.07 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16293 2951 4.9 %RANDOM
Rwork0.1413 ---
obs0.14235 57684 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.383 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.9→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 23 259 2863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022685
X-RAY DIFFRACTIONr_bond_other_d0.0020.022278
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9383654
X-RAY DIFFRACTIONr_angle_other_deg0.97535311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.84924.38137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3615415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0631513
X-RAY DIFFRACTIONr_chiral_restr0.0870.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02576
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_it1.1921.2841301
X-RAY DIFFRACTIONr_mcbond_other1.1921.281300
X-RAY DIFFRACTIONr_mcangle_it1.5731.9241628
X-RAY DIFFRACTIONr_mcangle_other1.5731.9271629
X-RAY DIFFRACTIONr_scbond_it1.71.4741382
X-RAY DIFFRACTIONr_scbond_other1.6991.4731383
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.952.1272027
X-RAY DIFFRACTIONr_long_range_B_refined2.20116.0023221
X-RAY DIFFRACTIONr_long_range_B_other2.13215.7243177
X-RAY DIFFRACTIONr_rigid_bond_restr2.83134960
X-RAY DIFFRACTIONr_sphericity_free16.6325170
X-RAY DIFFRACTIONr_sphericity_bonded5.79354986
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19 201 -
Rwork0.145 4193 -
obs--100 %

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