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- PDB-1arm: CARBOXYPEPTIDASE A WITH ZN REPLACED BY HG -

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Basic information

Entry
Database: PDB / ID: 1arm
TitleCARBOXYPEPTIDASE A WITH ZN REPLACED BY HG
ComponentsHG-CARBOXYPEPTIDASE A=ALPHA= (COX)
KeywordsHYDROLASE / METALLOPROTEASE / CARBOXYPEPTIDASE
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 / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A ...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 / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / : / Carboxypeptidase A1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.76 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 17, 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
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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.ptnr2_auth_seq_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HG-CARBOXYPEPTIDASE A=ALPHA= (COX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7107
Polymers34,7221
Non-polymers9886
Water3,909217
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 HG-CARBOXYPEPTIDASE A=ALPHA= (COX) / MERCURY REPLACED CPA


Mass: 34721.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00730, carboxypeptidase A
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsA TRIS SOLVENT MOLECULE (RESIDUE 309) IS BOUND IN THE ACTIVE SITE TO THE HG CATION AT 40% ...A TRIS SOLVENT MOLECULE (RESIDUE 309) IS BOUND IN THE ACTIVE SITE TO THE HG CATION AT 40% OCCUPANCY, AND A WATER MOLECULE IS ALSO BOUND TO THE HG CATION AT 60% OCCUPANCY. THERE ARE THREE OTHER BINDING SITES FOR MERCURY CATIONS ON CPA (RESIDUES 316 - 318). AN ADDITIONAL CATION IS BOUND TO GLU 270, AND IS ARBITRARILY LABELLED A COPPER CATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.47 %
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: Apr 17, 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 4 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.0908
Reflection
*PLUS
Highest resolution: 1.74 Å / Num. obs: 26225 / % possible obs: 82 % / Observed criterion σ(I): 0 / Num. measured all: 107065

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Processing

Software
NameClassification
TNTrefinement
PROLSQrefinement
P.A.TUCKERdata collection
P.A.TUCKERdata reduction
RefinementResolution: 1.76→12.1 Å / Isotropic thermal model: STANDARD TNT / σ(F): 0 / Stereochemistry target values: STANDARD TNT
Details: THESE LAST 7 CYCLES OF TNT REFINEMENT WERE RUN AFTER THE PROLSQ REFINEMENT.
Num. reflection% reflection
all26751 -
obs26751 91 %
Solvent computationSolvent model: DUE TO LACK OF LOW RES. DATA, KSOL WAS SUPPLIED.
Bsol: 224.7 Å2 / ksol: 0.71 e/Å3
Refinement stepCycle: LAST / Resolution: 1.76→12.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 13 217 2666
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01725110.8
X-RAY DIFFRACTIONt_angle_deg2.7634041.3
X-RAY DIFFRACTIONt_dihedral_angle_d16.114430
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_it7.8425040
X-RAY DIFFRACTIONt_nbd0.041810
Software
*PLUS
Name: TNT / Version: 5-E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.146
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.017 / Weight: 5

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