[English] 日本語
Yorodumi
- PDB-1qnh: Plasmodium falciparum Cyclophilin (double mutant) complexed with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qnh
TitlePlasmodium falciparum Cyclophilin (double mutant) complexed with Cyclosporin A
Components
  • CYCLOSPORIN A
  • PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
KeywordsISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT / CYCLOPHILIN
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cyclosporin A / : / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
TOLYPOCLADIUM INFLATUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPeterson, M.R. / Hall, D.R. / Hunter, W.N.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The Three-Dimensional Structure of a Plasmodium Falciparum Cyclophilin in Complex with the Potent Anti-Malarial Cyclosporin A
Authors: Peterson, M.R. / Hall, D.R. / Berriman, M. / Leonard, G.A. / Fairlamb, A.H. / Hunter, W.N.
#1: Journal: Biochem.J. / Year: 1998
Title: Detailed Characterization of a Cyclophilin from the Human Malaria Parasite Plasmodium Falciparum
Authors: Berriman, M. / Fairlamb, A.H.
History
DepositionOct 14, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2000Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
C: CYCLOSPORIN A
D: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)40,2104
Polymers40,2104
Non-polymers00
Water3,837213
1
A: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
C: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)20,1052
Polymers20,1052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8.2 kcal/mol
Surface area9520 Å2
MethodPQS
2
B: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
D: CYCLOSPORIN A


Theoretical massNumber of molelcules
Total (without water)20,1052
Polymers20,1052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-8.4 kcal/mol
Surface area9470 Å2
MethodPQS
Unit cell
Length a, b, c (Å)92.110, 115.120, 39.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.16335, -0.98606, 0.03182), (0.96489, -0.1664, -0.20321), (0.20567, -0.0025, 0.97862)
Vector: 63.67295, 72.66035, 11.18299)

-
Components

#1: Protein PEPTIDYL-PROLYL CIS-TRANS ISOMERASE / PPIASE / ROTAMASE / CYCLOPHILIN A


Mass: 18884.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q25756, peptidylprolyl isomerase
#2: Protein/peptide CYCLOSPORIN A / CYCLOSPORINE / CICLOSPORIN / CICLOSPORINE


Type: Cyclic peptide / Class: Immunosuppressant / Mass: 1220.625 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI.
Source: (synth.) TOLYPOCLADIUM INFLATUM (fungus) / References: NOR: NOR00033, Cyclosporin A
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) ...CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: CYCLOSPORIN A CHAIN: C, D COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 11 DESCRIPTION: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.7 / Details: pH 7.70
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein/drug complex1drop
235 mMHEPES1drop
315 %(w/v)PEG15001drop
430 %(w/v)PEG15001reservoir

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98
DetectorType: FUJI BAS-2000 IMAGE PLATE / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→24 Å / Num. obs: 24606 / % possible obs: 98.2 % / Redundancy: 5 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.8
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 3.7 / % possible all: 92.7

-
Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CWA

1cwa


Resolution: 2.1→24 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFINEMENT AT EARLY STAGES UTILISED X-PLOR AND REFMAC AND NCS RESTRAINTS WERE RELEASED AT THE FINAL STAGES OF REFINEMENT THE SIDE CHAINS OF THE FOLLOWING RESIDUES ARE DISORDERED ASN A 15, ...Details: REFINEMENT AT EARLY STAGES UTILISED X-PLOR AND REFMAC AND NCS RESTRAINTS WERE RELEASED AT THE FINAL STAGES OF REFINEMENT THE SIDE CHAINS OF THE FOLLOWING RESIDUES ARE DISORDERED ASN A 15, LYS A 51, LYS A 155, ARG B 49, LYS B 51, ARG B 88, LYS B 155, LYS B 160 SER A 2 IS DISORDERED AND NOT OBSERVED
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2471 10 %RANDOM
Rwork0.17 ---
obs0.17 24606 98.2 %-
Displacement parametersBiso mean: 26.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 0 0 213 2988
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.9171.5
X-RAY DIFFRACTIONc_mcangle_it1.3452
X-RAY DIFFRACTIONc_scbond_it1.5482
X-RAY DIFFRACTIONc_scangle_it2.0212.5
LS refinement shellResolution: 2.1→2.11 Å / Total num. of bins used: 49
RfactorNum. reflection% reflection
Rfree0.242 53 10 %
Rwork0.227 390 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

+
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