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- PDB-5lrg: Crystal structure of the porcine carboxypeptidase B - Anabaenopep... -

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Basic information

Entry
Database: PDB / ID: 5lrg
TitleCrystal structure of the porcine carboxypeptidase B - Anabaenopeptin B complex
Components
  • Anabaenopeptin B
  • Carboxypeptidase B
KeywordsHYDROLASE / Drug discovery / Natural compound / Tafi inhibitor / Anabaenopeptin
Function / homology
Function and homology information


carboxypeptidase B / metallocarboxypeptidase activity / cytoplasmic vesicle / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Carboxypeptidase B, 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 B, 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 speciesSus scrofa (pig)
Planktothrix rubescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsSchreuder, H. / Liesum, A. / Loenze, P.
CitationJournal: Sci Rep / Year: 2016
Title: Isolation, Co-Crystallization and Structure-Based Characterization of Anabaenopeptins as Highly Potent Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (TAFIa).
Authors: Schreuder, H. / Liesum, A. / Lonze, P. / Stump, H. / Hoffmann, H. / Schiell, M. / Kurz, M. / Toti, L. / Bauer, A. / Kallus, C. / Klemke-Jahn, C. / Czech, J. / Kramer, D. / Enke, H. / ...Authors: Schreuder, H. / Liesum, A. / Lonze, P. / Stump, H. / Hoffmann, H. / Schiell, M. / Kurz, M. / Toti, L. / Bauer, A. / Kallus, C. / Klemke-Jahn, C. / Czech, J. / Kramer, D. / Enke, H. / Niedermeyer, T.H. / Morrison, V. / Kumar, V. / Bronstrup, M.
History
DepositionAug 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_torsion / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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_conn_type.id
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxypeptidase B
B: Carboxypeptidase B
C: Carboxypeptidase B
F: Anabaenopeptin B
G: Anabaenopeptin B
H: Anabaenopeptin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9819
Polymers106,7856
Non-polymers1963
Water31,6341756
1
A: Carboxypeptidase B
F: Anabaenopeptin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6603
Polymers35,5952
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-41 kcal/mol
Surface area12030 Å2
MethodPISA
2
B: Carboxypeptidase B
G: Anabaenopeptin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6603
Polymers35,5952
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-42 kcal/mol
Surface area11940 Å2
MethodPISA
3
C: Carboxypeptidase B
H: Anabaenopeptin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6603
Polymers35,5952
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-41 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.780, 124.780, 48.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Carboxypeptidase B /


Mass: 34739.859 Da / Num. of mol.: 3 / Fragment: UNP residues 111-416 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Pancreas / References: UniProt: P09955, carboxypeptidase B
#2: Protein/peptide Anabaenopeptin B


Mass: 854.992 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Planktothrix rubescens (bacteria) / Strain: CBT287
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 1756 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1ul 16 mg/ml Protein with 40 mM Epsilon-amino caproic acid in water was equilibrated agains 14-20% PEG8000, 100 mM K-Cacodylate, pH 6.5 in a hanging drop Setup. The complex was prepared by ...Details: 1ul 16 mg/ml Protein with 40 mM Epsilon-amino caproic acid in water was equilibrated agains 14-20% PEG8000, 100 mM K-Cacodylate, pH 6.5 in a hanging drop Setup. The complex was prepared by soaking a CPB Crystal overnight in a drop of Reservoir solution with 10 mM Anabaenopeptin.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.02→54.04 Å / Num. obs: 54773 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.6
Reflection shellResolution: 2.02→2.08 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 3.4 / % possible all: 97.6

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Processing

Software
NameClassification
CNXrefinement
XDSdata reduction
XSCALEdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NSA

1nsa


Resolution: 2.02→54.04 Å / Data cutoff high absF: 10000 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2739 5 %Random selection
Rwork0.176 ---
obs-54769 98.09 %-
Displacement parametersBiso mean: 18.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.948 Å2-0.409 Å20 Å2
2--0.948 Å20 Å2
3----1.897 Å2
Refinement stepCycle: LAST / Resolution: 2.02→54.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7488 0 3 1756 9247
LS refinement shellResolution: 2.02→2.11 Å
RfactorNum. reflection% reflection
Rfree0.2441 342 5 %
Rwork0.2094 6495 -

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