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- PDB-1ee3: Cadmium-substituted bovine pancreatic carboxypeptidase A (alfa-fo... -

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Basic information

Entry
Database: PDB / ID: 1ee3
TitleCadmium-substituted bovine pancreatic carboxypeptidase A (alfa-form) at pH 7.5 and 2 mM chloride in monoclinic crystal form
ComponentsPROTEIN (CARBOXYPEPTIDASE A)
KeywordsHYDROLASE / ALFA/BETA FOLD
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
: / Carboxypeptidase A1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJensen, F. / Bukrinsky, T. / Bjerrum, J. / Larsen, S.
Citation
Journal: J.BIOL.INORG.CHEM. / Year: 2002
Title: Three high-resolution crystal structures of cadmium-substituted carboxypeptidase A provide insight into the enzymatic function
Authors: Jensen, F. / Bukrinsky, T. / Bjerrum, J. / Larsen, S.
#1: Journal: 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.T. / Kadziola, A.
#2: Journal: 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.
#3: Journal: Biochemistry / Year: 1997
Title: Structure and Dynamics of the Metal Site of Cadmium-substituted Carboxypeptidase A in Solution and Crystalline States and under Steady-State Peptide Hydrolysis
Authors: Bauer, R. / Danielsen, E. / Hemmingsen, L. / Soerensen, M.V. / Ulstrup, J. / Friis, E.P. / Auld, D.S. / Bjerrum, M.J.
History
DepositionJan 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_alt_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: PROTEIN (CARBOXYPEPTIDASE A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1715
Polymers34,7221
Non-polymers4504
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.178, 60.205, 51.715
Angle α, β, γ (deg.)90.00, 97.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (CARBOXYPEPTIDASE A)


Mass: 34721.750 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: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.12 Å3/Da / Density % sol: 32 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 7.5
Details: Lithium Chloride, Tris-HNO3, Cadmium Chloride, pH 7.5, MICRODIALYSIS, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.0 M11LiCl
220 mMTris-HNO311pH7.5
320 mg/mlprotein11
40.35 M12LiCl
520 mMTris-HNO312pH7.5

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 15, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 31210 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 29
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 5.4 / % possible all: 84.9
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 40 Å / Num. measured all: 348864
Reflection shell
*PLUS
% possible obs: 84.9 %

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Processing

Software
NameClassification
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CPA.PDB

5cpa


Resolution: 1.7→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: MAXIMUM LIKELIHOOD MINIMIZATION OF THE STRUCTURE FACTOR AMPLITUDE DIFFERENCES.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1591 5 %RANDOM
Rwork0.174 ---
obs0.174 31210 98.4 %-
Solvent computationSolvent model: CNS MASK / Bsol: 33.7 Å2 / ksol: 0.317 e/Å3
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 5 245 2678
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.28
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.707
X-RAY DIFFRACTIONc_mcangle_it1.072
X-RAY DIFFRACTIONc_scbond_it1.297
X-RAY DIFFRACTIONc_scangle_it1.841
LS refinement shellResolution: 1.7→1.72 Å / Total num. of bins used: 31
RfactorNum. reflection% reflection
Rfree0.363 52 5 %
Rwork0.278 828 -
obs--85 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.1978 / Rfactor Rwork: 0.1737
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0055
LS refinement shell
*PLUS
% reflection Rfree: 5 %

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