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- PDB-4gm5: Carboxypeptidase T with Sulphamoil Arginine -

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Basic information

Entry
Database: PDB / ID: 4gm5
TitleCarboxypeptidase T with Sulphamoil Arginine
ComponentsCarboxypeptidase T
KeywordsHYDROLASE/HYDROLASE inhibitor / Zinc carboxypeptidase / HYDROLASE-HYDROLASE inhibitor complex
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
N~2~-sulfamoyl-L-arginine / Carboxypeptidase T
Similarity search - Component
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsKuznetsov, S.A. / Timofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
CitationJournal: To be Published
Title: Carboxypeptidase T with Sulphamoil Arginine
Authors: Kuznetsov, S.A. / Timofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
History
DepositionAug 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: 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 / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)39,09028
Polymers36,6411
Non-polymers2,44927
Water7,350408
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carboxypeptidase T
hetero molecules

A: Carboxypeptidase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,18056
Polymers73,2832
Non-polymers4,89754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area9430 Å2
ΔGint-341 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.050, 158.050, 104.980
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-590-

HOH

21A-634-

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 / Fragment: unp residues 99-421
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 , 6 types, 435 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.: 9 / 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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

CrystalDensity Matthews: 5.17 Å3/Da / Density % sol: 76.19 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.388→26.95 Å / Num. all: 152576 / Num. obs: 151202 / % possible obs: 99.1 % / Redundancy: 4.97 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.7916

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→20 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.35 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16225 7646 5 %RANDOM
Rwork0.14227 ---
obs0.14327 144836 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.129 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.37 Å2-0 Å2
2--0.37 Å2-0 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.39→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 138 408 3127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193051
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9754163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.335381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.67324.558147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.03815460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3331514
X-RAY DIFFRACTIONr_chiral_restr0.0890.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212394
X-RAY DIFFRACTIONr_rigid_bond_restr2.01833049
X-RAY DIFFRACTIONr_sphericity_free34.368534
X-RAY DIFFRACTIONr_sphericity_bonded16.18953365
LS refinement shellResolution: 1.388→1.424 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 521 -
Rwork0.304 10617 -
obs--99.04 %

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