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- PDB-1ka2: Structure of Pyrococcus furiosus Carboxypeptidase Apo-Mg -

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Basic information

Entry
Database: PDB / ID: 1ka2
TitleStructure of Pyrococcus furiosus Carboxypeptidase Apo-Mg
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.3Aug 16, 2023Group: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

Downloads & links

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Assembly

Deposited unit
A: M32 carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1522
Polymers59,1281
Non-polymers241
Water1,964109
1
A: M32 carboxypeptidase
hetero molecules

A: M32 carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3044
Polymers118,2552
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y,-z+31
Unit cell
Length a, b, c (Å)130.515, 67.106, 67.885
Angle α, β, γ (deg.)90.00, 95.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein M32 carboxypeptidase


Mass: 59127.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U3L0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.55 Å3/Da / Density % sol: 51.43 %
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: NSLS / Beamline: X4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 1999
RadiationMonochromator: KOHZU double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 29834 / Num. obs: 29834 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.278 / % possible all: 95.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 147392 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 95.1 % / Rmerge(I) obs: 0.278

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1k9x

1k9x


Resolution: 2.2→19.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 274479.57 / 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
Rfree0.284 2983 9.9 %RANDOM
Rwork0.239 ---
all0.239 29834 --
obs0.239 29834 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.5056 Å2 / ksol: 0.400947 e/Å3
Displacement parametersBiso mean: 42.9 Å2
Baniso -1Baniso -2Baniso -3
1-18.06 Å20 Å25.38 Å2
2---10.67 Å20 Å2
3----7.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4163 0 1 109 4273
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.842.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 398 9.5 %
Rwork0.306 3810 -
obs--95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / % reflection Rfree: 10 % / Rfactor obs: 0.239 / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.63
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.337 / Rfactor Rwork: 0.306

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