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- PDB-5wvu: Crystal structure of carboxypeptidase from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 5wvu
TitleCrystal structure of carboxypeptidase from Thermus thermophilus
ComponentsThermostable carboxypeptidase 1
KeywordsHYDROLASE / carboxypeptidase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


carboxypeptidase Taq / metallocarboxypeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Peptidase M32, carboxypeptidase Taq / Carboxypeptidase Taq (M32) metallopeptidase / Peptidase family M32 domain profile. / Neurolysin; domain 3 - #30 / Neurolysin; domain 3 / Neutral zinc metallopeptidases, zinc-binding region signature. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Thermostable carboxypeptidase 1
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsOkai, M. / Nagata, K. / Tanokura, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Insight into the transition between the open and closed conformations of Thermus thermophilus carboxypeptidase.
Authors: Okai, M. / Yamamura, A. / Hayakawa, K. / Tsutsui, S. / Miyazono, K.I. / Lee, W.C. / Nagata, K. / Inoue, Y. / Tanokura, M.
History
DepositionDec 29, 2016Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 22, 2017ID: 1WGZ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thermostable carboxypeptidase 1
B: Thermostable carboxypeptidase 1
C: Thermostable carboxypeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,83010
Polymers174,2663
Non-polymers5657
Water4,035224
1
A: Thermostable carboxypeptidase 1
hetero molecules

A: Thermostable carboxypeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,86010
Polymers116,1772
Non-polymers6838
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4640 Å2
ΔGint-74 kcal/mol
Surface area41260 Å2
MethodPISA
2
B: Thermostable carboxypeptidase 1
C: Thermostable carboxypeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4005
Polymers116,1772
Non-polymers2233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-80 kcal/mol
Surface area40100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.100, 233.700, 124.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Thermostable carboxypeptidase 1 / TthCP1


Mass: 58088.543 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: TTHA0270 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SLM3, carboxypeptidase Taq
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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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: 3.55 Å3/Da / Density % sol: 65.32 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 8000, posodium chloride, magnesium chloride, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→41.245 Å / Num. obs: 75787 / % possible obs: 99.4 % / Redundancy: 3.7 % / Net I/σ(I): 6.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.6→41.245 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.13
RfactorNum. reflection% reflection
Rfree0.2339 3798 5.02 %
Rwork0.1901 --
obs0.1924 75730 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→41.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12336 0 27 224 12587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01412710
X-RAY DIFFRACTIONf_angle_d1.24517249
X-RAY DIFFRACTIONf_dihedral_angle_d16.3027550
X-RAY DIFFRACTIONf_chiral_restr0.0541764
X-RAY DIFFRACTIONf_plane_restr0.0092289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5998-2.63270.3311310.25332592X-RAY DIFFRACTION98
2.6327-2.66740.28491320.24022620X-RAY DIFFRACTION98
2.6674-2.70390.27341410.23332595X-RAY DIFFRACTION98
2.7039-2.74250.28211350.23442608X-RAY DIFFRACTION98
2.7425-2.78350.33531230.25052640X-RAY DIFFRACTION99
2.7835-2.82690.30621540.24832606X-RAY DIFFRACTION99
2.8269-2.87330.28541410.24532615X-RAY DIFFRACTION99
2.8733-2.92280.2991520.24222606X-RAY DIFFRACTION99
2.9228-2.97590.30311260.23992682X-RAY DIFFRACTION99
2.9759-3.03320.28741470.23612641X-RAY DIFFRACTION99
3.0332-3.09510.29341390.22132621X-RAY DIFFRACTION99
3.0951-3.16230.291330.23382665X-RAY DIFFRACTION100
3.1623-3.23590.28981530.22822638X-RAY DIFFRACTION99
3.2359-3.31680.28271360.22922649X-RAY DIFFRACTION100
3.3168-3.40640.27341530.21322659X-RAY DIFFRACTION100
3.4064-3.50660.23611230.19852699X-RAY DIFFRACTION100
3.5066-3.61970.21411370.18962674X-RAY DIFFRACTION100
3.6197-3.7490.22331420.17882672X-RAY DIFFRACTION100
3.749-3.8990.22341180.18992717X-RAY DIFFRACTION100
3.899-4.07630.24721370.18842665X-RAY DIFFRACTION100
4.0763-4.2910.24041370.17272705X-RAY DIFFRACTION100
4.291-4.55950.18611380.14992702X-RAY DIFFRACTION100
4.5595-4.9110.16051520.13752687X-RAY DIFFRACTION100
4.911-5.40430.20141690.14712701X-RAY DIFFRACTION100
5.4043-6.1840.22411550.16592705X-RAY DIFFRACTION100
6.184-7.78260.17911380.1582766X-RAY DIFFRACTION100
7.7826-41.25020.18321560.16322802X-RAY DIFFRACTION98

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