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- PDB-6f79: Carboxypeptidase T mutant L211Q with Sulphamoil Arginine -

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Basic information

Entry
Database: PDB / ID: 6f79
TitleCarboxypeptidase T mutant L211Q 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTimofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
CitationJournal: To Be Published
Title: Carboxypeptidase T mutant L211Q with Sulphamoil Arginine
Authors: Timofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
History
DepositionDec 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 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 13, 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)37,36710
Polymers36,6561
Non-polymers7119
Water6,179343
1
A: Carboxypeptidase T
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)224,20560
Polymers219,9376
Non-polymers4,26754
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_455-x+y-1,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area18620 Å2
ΔGint-692 kcal/mol
Surface area59760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.960, 157.960, 104.850
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-639-

HOH

21A-665-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carboxypeptidase T


Mass: 36656.246 Da / Num. of mol.: 1 / Mutation: L211Q
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, 352 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.: 2 / 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.: 343 / 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: 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 6M / Detector: PIXEL / Date: Dec 4, 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: 60927 / % possible obs: 99.99 % / Redundancy: 20.62 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 4.4391
Reflection shellResolution: 1.9→2 Å / Redundancy: 20.89 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.75 / Num. unique obs: 8747 / % 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→29.85 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.578 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14715 2961 4.9 %RANDOM
Rwork0.12696 ---
obs0.12794 57912 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.909 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.9→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 32 343 2957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022726
X-RAY DIFFRACTIONr_bond_other_d0.0020.022291
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9423715
X-RAY DIFFRACTIONr_angle_other_deg0.95935350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.99724.42138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18915420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2641513
X-RAY DIFFRACTIONr_chiral_restr0.0830.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213106
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02586
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_it0.7881.3141321
X-RAY DIFFRACTIONr_mcbond_other0.7841.311320
X-RAY DIFFRACTIONr_mcangle_it0.9741.9681660
X-RAY DIFFRACTIONr_mcangle_other0.9741.9731661
X-RAY DIFFRACTIONr_scbond_it1.1011.4961403
X-RAY DIFFRACTIONr_scbond_other1.0321.471396
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.112.1332043
X-RAY DIFFRACTIONr_long_range_B_refined2.02616.9833377
X-RAY DIFFRACTIONr_long_range_B_other1.72616.0653283
X-RAY DIFFRACTIONr_rigid_bond_restr0.9635014
X-RAY DIFFRACTIONr_sphericity_free18.8675222
X-RAY DIFFRACTIONr_sphericity_bonded3.84855071
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.157 202 -
Rwork0.121 4209 -
obs--99.98 %

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