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- PDB-1m4l: STRUCTURE OF NATIVE CARBOXYPEPTIDASE A AT 1.25 RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1m4l
TitleSTRUCTURE OF NATIVE CARBOXYPEPTIDASE A AT 1.25 RESOLUTION
ComponentsCARBOXYPEPTIDASE A
KeywordsHYDROLASE / CARBOXYPEPTIDASE A / METALLOPROTEINASE / METALLOEXOPROTEINASE
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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsKilshtain-Vardi, A. / Glick, M. / Greenblatt, H.M. / Goldblum, A. / Shoham, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Refined structure of bovine carboxypeptidase A at 1.25 A resolution.
Authors: Kilshtain-Vardi, A. / Glick, M. / Greenblatt, H.M. / Goldblum, A. / Shoham, G.
History
DepositionJul 3, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_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_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_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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBOXYPEPTIDASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5112
Polymers34,4451
Non-polymers651
Water6,756375
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.687, 60.267, 47.453
Angle α, β, γ (deg.)90.00, 97.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CARBOXYPEPTIDASE A


Mass: 34445.418 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.82 Å3/Da / Density % sol: 32.4 %
Crystal grow
*PLUS
Temperature: 5 ℃ / pH: 7.5 / Method: microdialysis
Details: Shoham, G., (1988) Proc.Natl.Acad.Sci.USA., 85, 684.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.0 M11LiCl
20.03 MTris-HCl11pH7.5
30.2 M12LiCl
40.03 MTris-HCl11pH7.5

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.085 / Wavelength: 1.085 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.085 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. all: 64976 / Num. obs: 64976 / % possible obs: 86.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.5
Reflection shellResolution: 1.25→1.27 Å / Rmerge(I) obs: 0.127 / % possible all: 36.3
Reflection
*PLUS
Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 36.3 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
SHELXL-97refinement
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTERY 1YME

1yme


Resolution: 1.25→30 Å / Num. parameters: 25563 / Num. restraintsaints: 31254 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.05.
RfactorNum. reflection% reflectionSelection details
Rfree0.1451 3416 5.3 %RANDOM
Rwork0.104 ---
all0.104 64976 --
obs-64976 86.3 %-
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2764.4
Refinement stepCycle: LAST / Resolution: 1.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 0 1 375 2838
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0268
X-RAY DIFFRACTIONs_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.08
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.056
X-RAY DIFFRACTIONs_approx_iso_adps0.102
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_chiral_restr0.10.076

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