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- PDB-3hoa: Crystal structure of the Thermus thermophilus M32 carboxypeptidase -

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Basic information

Entry
Database: PDB / ID: 3hoa
TitleCrystal structure of the Thermus thermophilus M32 carboxypeptidase
ComponentsThermostable carboxypeptidase 1
KeywordsHYDROLASE / proline-rich loop / Carboxypeptidase
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Metal-dependent carboxypeptidase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLee, M.M. / Chan, M.K.
CitationJournal: Proteins / Year: 2009
Title: Insight into the substrate length restriction of M32 carboxypeptidases: Characterization of two distinct subfamilies.
Authors: Lee, M.M. / Isaza, C.E. / White, J.D. / Chen, R.P. / Liang, G.F. / He, H.T. / Chan, S.I. / Chan, M.K.
History
DepositionJun 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 31, 2021Group: Data collection / Derived calculations / Category: reflns / reflns_shell / struct_site
Item: _reflns.pdbx_redundancy / _reflns_shell.pdbx_redundancy ..._reflns.pdbx_redundancy / _reflns_shell.pdbx_redundancy / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,1553
Polymers116,0632
Non-polymers921
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-11.2 kcal/mol
Surface area40970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.610, 84.330, 109.050
Angle α, β, γ (deg.)90.00, 93.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thermostable carboxypeptidase 1


Mass: 58031.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / DSM 7039 / Gene: TT_C1715 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q72GY3, carboxypeptidase Taq
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M Na-citrate pH 4.0, 8% w/v PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.00002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2003
Details: 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.1→45.7 Å / Num. all: 60029 / Num. obs: 60029 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.417 % / Biso Wilson estimate: 2.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 20.4
Reflection shellResolution: 2.1→2.23 Å / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 5.1 / Num. unique all: 8712 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Bacillus subtilis carboxypeptidase

Resolution: 2.1→19.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 132243.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 6100 10.2 %RANDOM
Rwork0.218 ---
all0.223 60029 --
obs0.223 60029 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.7339 Å2 / ksol: 0.380191 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20 Å22.22 Å2
2---1.92 Å20 Å2
3---0.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8216 0 6 467 8689
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 973 10 %
Rwork0.218 8712 -
obs--94.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2glycerol.param
X-RAY DIFFRACTION3water_rep.param

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