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- PDB-1k9x: Structure of Pyrococcus furiosus carboxypeptidase Apo-Yb -

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Basic information

Entry
Database: PDB / ID: 1k9x
TitleStructure of Pyrococcus furiosus carboxypeptidase Apo-Yb
ComponentsM32 carboxypeptidase
Keywordscarboxypeptidase / HEXXH motif / M32 family / metallopeptidase
Function / homology
Function and homology information


carboxypeptidase Taq / cobalt ion binding / metallocarboxypeptidase activity / proteolysis
Similarity search - Function
Peptidase family M32 domain profile. / Peptidase M32, carboxypeptidase Taq / Carboxypeptidase Taq (M32) metallopeptidase / 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 speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsArndt, J.W. / Hao, B. / Ramakrishnan, V. / Cheng, T. / Chan, S.I. / Chan, M.K.
CitationJournal: Structure / Year: 2002
Title: Crystal Structure of a Novel Carboxypeptidase from the Hyperthermophilic Archaeon Pyrococcus furiosus
Authors: Arndt, J.W. / Hao, B. / Ramakrishnan, V. / Cheng, T. / Chan, S.I. / Chan, M.K.
History
DepositionOct 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE An appropriate sequence database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M32 carboxypeptidase
B: M32 carboxypeptidase
C: M32 carboxypeptidase
D: M32 carboxypeptidase


Theoretical massNumber of molelcules
Total (without water)236,5114
Polymers236,5114
Non-polymers00
Water10,971609
1
A: M32 carboxypeptidase
D: M32 carboxypeptidase


Theoretical massNumber of molelcules
Total (without water)118,2552
Polymers118,2552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-10 kcal/mol
Surface area40190 Å2
MethodPISA
2
B: M32 carboxypeptidase
C: M32 carboxypeptidase


Theoretical massNumber of molelcules
Total (without water)118,2552
Polymers118,2552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-12 kcal/mol
Surface area40250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.342, 86.780, 107.895
Angle α, β, γ (deg.)88.64, 78.54, 69.44
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
M32 carboxypeptidase


Mass: 59127.664 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U3L0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.45 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, TRIS, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
119 mg/mlprotein1drop
250 mMTris1droppH8.0
310 %glycerol1drop
425-30 %PEG40001reservoir
5100 mMTris1reservoirpH8.5
620-40 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.0000, 1.3860
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2000
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.3861
ReflectionResolution: 2.3→50 Å / Num. all: 98094 / Num. obs: 98094 / % possible obs: 93.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 26.2
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.087 / % possible all: 80.5
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 353793 / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 80.5 % / Rmerge(I) obs: 0.087

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→48.78 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 285605.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 9809 10.1 %RANDOM
Rwork0.212 ---
all0.212 98094 --
obs0.212 98094 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.6958 Å2 / ksol: 0.325539 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.76 Å2-4.11 Å21.4 Å2
2---1.89 Å2-0.66 Å2
3----1.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16652 0 0 609 17261
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 1199 9.6 %
Rwork0.231 11277 -
obs--80.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / % reflection Rfree: 10 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.237
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor Rfree: 0.327 / Rfactor Rwork: 0.231

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