[English] 日本語
Yorodumi
- PDB-5lrj: Crystal structure of the porcine carboxypeptidase B - Anabaenopep... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lrj
TitleCrystal structure of the porcine carboxypeptidase B - Anabaenopeptin C complex
Components
  • Anabaenopeptin C
  • 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. / Zn_pept / Peptidase family M14 domain profile. / 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. / Zn_pept / Peptidase family M14 domain profile. / 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: 2.2 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,8979
Polymers106,7016
Non-polymers1963
Water26,2481457
1
A: Carboxypeptidase B
F: Anabaenopeptin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6323
Polymers35,5672
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-42 kcal/mol
Surface area11880 Å2
MethodPISA
2
B: Carboxypeptidase B
G: Anabaenopeptin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6323
Polymers35,5672
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-41 kcal/mol
Surface area11910 Å2
MethodPISA
3
C: Carboxypeptidase B
H: Anabaenopeptin C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6323
Polymers35,5672
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-41 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.960, 124.960, 48.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
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 C


Mass: 826.979 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


Mass: 18.015 Da / Num. of mol.: 1457 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1 ul of a solution of 16 mg/ml CPB with 40 mM epsilon-amino caproic acid in water was equilibrated against 14-20% PEG8000 in 100 mM MES (pH 6.0) using a hanging drop Setup.

-
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: Sep 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→48.12 Å / Num. obs: 42541 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.7
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.321 / % possible all: 99.5

-
Processing

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

1nsa


Resolution: 2.2→48.12 Å / Data cutoff high absF: 10000 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2127 5 %Random
Rwork0.152 ---
obs-42541 99.7 %-
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.528 Å2-1.182 Å20 Å2
2--0.528 Å20 Å2
3----1.057 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7482 0 3 1457 8942
LS refinement shellResolution: 2.2→2.3 Å
RfactorNum. reflection% reflection
Rfree0.2377 267 5 %
Rwork0.1914 5074 -

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more