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- PDB-1arl: CARBOXYPEPTIDASE A WITH ZN REMOVED -

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Basic information

Entry
Database: PDB / ID: 1arl
TitleCARBOXYPEPTIDASE A WITH ZN REMOVED
ComponentsAPO-CARBOXYPEPTIDASE A=ALPHA= (COX)
KeywordsCARBOXYPEPTIDASE / METALLOPROTEINASE / HYDROLASE
Function / homology
Function and homology information


carboxypeptidase A / leukotriene metabolic process / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase ...Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.88 Å
AuthorsGreenblatt, H.M. / Feinberg, H. / Tucker, P.A. / Shoham, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Carboxypeptidase A: native, zinc-removed and mercury-replaced forms.
Authors: Greenblatt, H.M. / Feinberg, H. / Tucker, P.A. / Shoham, G.
History
DepositionNov 22, 1994Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification / _software.name
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APO-CARBOXYPEPTIDASE A=ALPHA= (COX)


Theoretical massNumber of molelcules
Total (without water)34,4451
Polymers34,4451
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.700, 60.320, 47.200
Angle α, β, γ (deg.)90.00, 97.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein APO-CARBOXYPEPTIDASE A=ALPHA= (COX) / ZINC REMOVED CPA


Mass: 34445.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00730, carboxypeptidase A
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: microdialysis
Details: Shoham, G., (1984) Proc. Natl. Acad. Sci. USA., 81, 7767.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 M11NaCl
20.03 MTris-HCl11

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MACSCIENCE DIP100 / Detector: IMAGE PLATE / Date: Mar 23, 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 21540 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 3.74 Å2 / Rmerge(I) obs: 0.065
Reflection
*PLUS
Highest resolution: 1.86 Å / Num. measured all: 84305 / Rmerge(I) obs: 0.0654

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Processing

Software
NameClassification
TNTrefinement
PROLSQrefinement
P.A.TUCKERdata collection
P.A.TUCKERdata reduction
RefinementResolution: 1.88→13 Å / Isotropic thermal model: TNT / σ(F): 0 / Stereochemistry target values: TNT
RfactorNum. reflection% reflection
all0.143 21331 -
obs-21331 88 %
Solvent computationSolvent model: KSOL FIXED DUE TO LACK OF LOW RESOLUTION DATA
Bsol: 194.8 Å2 / ksol: 0.71 e/Å3
Refinement stepCycle: LAST / Resolution: 1.88→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2437 0 0 179 2616
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01625040.8
X-RAY DIFFRACTIONt_angle_deg2.7933951.3
X-RAY DIFFRACTIONt_dihedral_angle_d17.314400
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.013552
X-RAY DIFFRACTIONt_gen_planes0.0173675
X-RAY DIFFRACTIONt_it8.39925040
X-RAY DIFFRACTIONt_nbd0.0642310
Software
*PLUS
Name: TNT / Version: 5-E / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0132
X-RAY DIFFRACTIONt_plane_restr0.0175

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