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

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Basic information

Entry
Database: PDB / ID: 5lrk
TitleCrystal structure of the porcine carboxypeptidase B - Anabaenopeptin F complex
Components
  • Anabaenopeptin F
  • 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: 2.3 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 / 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 F
G: Anabaenopeptin F
H: Anabaenopeptin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0239
Polymers106,8276
Non-polymers1963
Water17,997999
1
A: Carboxypeptidase B
F: Anabaenopeptin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6743
Polymers35,6092
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-41 kcal/mol
Surface area11960 Å2
MethodPISA
2
B: Carboxypeptidase B
G: Anabaenopeptin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6743
Polymers35,6092
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-41 kcal/mol
Surface area11900 Å2
MethodPISA
3
C: Carboxypeptidase B
H: Anabaenopeptin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6743
Polymers35,6092
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-41 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.620, 124.620, 48.470
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) / References: UniProt: P09955, carboxypeptidase B
#2: Protein/peptide Anabaenopeptin F


Mass: 869.019 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.: 999 / 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: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1ul of 16 mg/ml Protein and 40 mM epsilon-amino caproic acid in water were equilibrated against 14-20% PEG8000 and 100 mM K-Cacodylate (pH 6.5) in a hanging drop Setup.

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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: 2.3→62.24 Å / Num. obs: 37153 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.279 / % possible all: 99.3

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Processing

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

1nsa


Resolution: 2.3→62.24 Å / Data cutoff high absF: 10000 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1857 5 %Random
Rwork0.154 ---
obs-37137 99.3 %-
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.544 Å2-0.481 Å20 Å2
2--0.544 Å20 Å2
3----1.087 Å2
Refinement stepCycle: LAST / Resolution: 2.3→62.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7491 0 3 999 8493
LS refinement shellResolution: 2.3→2.4 Å
RfactorNum. reflection% reflection
Rfree0.2201 1857 5 %
Rwork0.1932 4398 -

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