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- PDB-1cpx: BETA FORM OF CARBOXYPEPTIDASE A (RESIDUES 3-307) FROM BOVINE PANC... -

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Basic information

Entry
Database: PDB / ID: 1cpx
TitleBETA FORM OF CARBOXYPEPTIDASE A (RESIDUES 3-307) FROM BOVINE PANCREAS IN AN ORTHORHOMBIC CRYSTAL FORM WITH TWO ZINC IONS IN THE ACTIVE SITE.
ComponentsPROTEIN (CARBOXYPEPTIDASE A)
KeywordsHYDROLASE / METALLOPROTEASE / CARBOXYPEPTIDASE / ZINC INHIBITION / INDUCED FIT
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. / Zn_pept / Peptidase family M14 domain profile. / 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. / Zn_pept / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HYDROXIDE ION / Carboxypeptidase A1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBukrinsky, J.T. / Bjerrum, M.J. / Kadziola, A.
CitationJournal: Biochemistry / Year: 1998
Title: Native carboxypeptidase A in a new crystal environment reveals a different conformation of the important tyrosine 248.
Authors: Bukrinsky, J.T. / Bjerrum, M.J. / Kadziola, A.
History
DepositionJul 27, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 5, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CARBOXYPEPTIDASE A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5934
Polymers34,4451
Non-polymers1483
Water4,990277
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.790, 66.850, 96.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (CARBOXYPEPTIDASE A) / E.C.3.4.17.1 HYDROLASE / CPA / BETA FORM


Mass: 34445.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: SIGMA #C0261; COX ET AL. (1964) BIOCHEMISTRY 3, 44-47
Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00730, carboxypeptidase A
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsZN 308 IS THE CATALYTIC ZINC AND ZN 309 IS THE INHIBITORY ZINC OH 541 IS THE HYDROXIDE ION, WHICH ...ZN 308 IS THE CATALYTIC ZINC AND ZN 309 IS THE INHIBITORY ZINC OH 541 IS THE HYDROXIDE ION, WHICH BRIDGES THE CATALYTIC ZINC (ZN 308) AND THE INHIBITORY ZINC (ZN309)
Sequence detailsSER 3 - ASN 307, I.E. THE BETA FORM OF CPA

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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: 2.25 Å3/Da / Density % sol: 45 %
Crystal growMethod: microdialysis / pH: 7.5
Details: CPA FROM SIGMA #C0261 WAS DISSOLVED IN 1.0 M LICL WITH 20 MM TRIS-HCL PH 7.5 TO GIVE 12 MG/ML AND USED WITHOUT FURTHER PURIFICATION. THIS PROTEIN SOLUTION WAS PLACED IN 50 MICROL DIALYSIS ...Details: CPA FROM SIGMA #C0261 WAS DISSOLVED IN 1.0 M LICL WITH 20 MM TRIS-HCL PH 7.5 TO GIVE 12 MG/ML AND USED WITHOUT FURTHER PURIFICATION. THIS PROTEIN SOLUTION WAS PLACED IN 50 MICROL DIALYSIS BUTTONS FROM HAMPTON RESEARCH AND DIALYZED AGAINST A 2 ML RESERVOIR OF THE ABOVE MENTIONED BUFFER WHILE LOWERING THE EXTERNAL LICL CONCENTRATION BY 25% EVERY OTHER DAY. THE CRYSTALS APPEARED A~0.24 M LICL AND WAS STORED AT 0.30M LICL. IF THIS PROCEDURE DOES NOT WORK BY ITSELF AND YOU END UP WITH THE MONOCLINIC ALPHA-FORM (1-307), YOU CAN TRY TO AD TRACES OF TRYPSIN (~10 MICROG/ML) TO THE PROTEIN SOLUTION TO PROVOKE FORMATION OF THE BETA-FORM (3-307), micro dialysis
Crystal
*PLUS
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.0 M11LiCl
220 mMTris-HCl11
30.24 M12LiCl

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Dec 6, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 20453 / % possible obs: 94.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 30.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 7.1 / Rsym value: 0.157 / % possible all: 67.7
Reflection shell
*PLUS
% possible obs: 67.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CPA WITHOUT WATERS AND ZN

5cpa


Resolution: 2→8 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 977 5 %RANDOM
Rwork0.167 ---
obs0.167 20060 93.4 %-
Displacement parametersBiso mean: 15.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-4.08 Å
Luzzati sigma a0.18 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2421 0 3 277 2701
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.001
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.238
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.2211.5
X-RAY DIFFRACTIONx_mcangle_it2.2772
X-RAY DIFFRACTIONx_scbond_it2.8762
X-RAY DIFFRACTIONx_scangle_it2.82.5
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.252 83 4.2 %
Rwork0.224 1878 -
obs--73.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION3PAR-CIS.PEPTOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.238
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.252 / % reflection Rfree: 4.2 % / Rfactor Rwork: 0.224

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