[English] 日本語
Yorodumi
- PDB-5jpf: Serine/Threonine phosphatase Z1 (Candida albicans) binds to inhib... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jpf
TitleSerine/Threonine phosphatase Z1 (Candida albicans) binds to inhibitor microcystin-LR
Components
  • Microcystin-LR
  • Serine/threonine-protein phosphatase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / yeast-specific serine/threonine phosphatase / microcystin-LR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


myosin phosphatase activity / protein-serine/threonine phosphatase / metal ion binding / cytoplasm
Similarity search - Function
Phosphoprotein phosphatase PPZ/Ppq1 / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type ...Phosphoprotein phosphatase PPZ/Ppq1 / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Microcystin LR / MALONATE ION / : / : / Serine/threonine-protein phosphatase
Similarity search - Component
Biological speciesCandida albicans (yeast)
Microcystis aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.39929733252 Å
AuthorsChoy, M.S. / Chen, E.H. / Peti, W. / Page, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098482 United States
CitationJournal: Mbio / Year: 2016
Title: Molecular Insights into the Fungus-Specific Serine/Threonine Protein Phosphatase Z1 in Candida albicans.
Authors: Chen, E. / Choy, M.S. / Petrenyi, K. / Konya, Z. / Erdodi, F. / Dombradi, V. / Peti, W. / Page, R.
History
DepositionMay 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_validate_polymer_linkage
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein phosphatase
M: Microcystin-LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4847
Polymers37,0682
Non-polymers4165
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-7 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.665, 50.665, 201.054
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

-
Components

#1: Protein Serine/threonine-protein phosphatase / Serine/threonine phosphatase Z1


Mass: 36053.473 Da / Num. of mol.: 1 / Fragment: UNP residues 171-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: CAWG_01946 / Production host: Escherichia coli (E. coli)
References: UniProt: C4YM68, protein-serine/threonine phosphatase
#2: Protein/peptide Microcystin-LR


Type: Oligopeptide / Class: Toxin / Mass: 1014.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Microcystis aeruginosa (bacteria) / References: NOR: NOR00109, Microcystin LR
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.19 Å3/Da / Density % sol: 38.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.1 / Details: 0.06 M citric acid, pH 4.1, 16% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 12331 / % possible obs: 98.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 31.3055033723 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.442.70.1975100.93284.2
2.44-2.492.80.1965281.0689.8
2.49-2.533.40.1816130.99596.5
2.53-2.593.90.1835910.9699.8
2.59-2.644.80.1576141.014100
2.64-2.76.20.1665931.055100
2.7-2.776.90.1516201.02100
2.77-2.8570.1336241.041100
2.85-2.936.80.1146061.074100
2.93-3.027.10.0956121.148100
3.02-3.136.90.0866201.192100
3.13-3.2670.0796121.32100
3.26-3.416.90.0716341.494100
3.41-3.5870.0646071.59499.8
3.58-3.816.70.0686472.746100
3.81-4.16.90.0576072.151100
4.1-4.526.70.056482.58100
4.52-5.1770.0456521.789100
5.17-6.516.90.056621.462100
6.51-506.40.0437311.9899.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.6 Å43.88 Å
Translation6.6 Å43.88 Å

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JPE

5jpe


Resolution: 2.39929733252→43.8771770827 Å / SU ML: 0.251334000047 / Cross valid method: FREE R-VALUE / σ(F): 1.34237012989 / Phase error: 22.1299322925
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234480797525 637 5.18602947163 %
Rwork0.178764472004 11646 -
obs0.181591154876 12283 98.5241036336 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.8085424173 Å2
Refinement stepCycle: LAST / Resolution: 2.39929733252→43.8771770827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 23 50 2458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003475379636682469
X-RAY DIFFRACTIONf_angle_d0.5672314091743331
X-RAY DIFFRACTIONf_chiral_restr0.0411586764162370
X-RAY DIFFRACTIONf_plane_restr0.00302714063993431
X-RAY DIFFRACTIONf_dihedral_angle_d10.99929242531425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3993-2.58450.3185959562791060.20574463392129X-RAY DIFFRACTION92.5849212925
2.5845-2.84460.2785925363031330.2197325534482317X-RAY DIFFRACTION100
2.8446-3.25610.2704851226971380.1956499415312306X-RAY DIFFRACTION100
3.2561-4.10180.1952047393481270.1678744374312359X-RAY DIFFRACTION100
4.1018-43.88450.2093995493541330.1584559633352535X-RAY DIFFRACTION99.925093633

+
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