[English] 日本語
Yorodumi
- PDB-2c3b: The Crystal Structure of Aspergillus fumigatus Cyclophilin reveal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2c3b
TitleThe Crystal Structure of Aspergillus fumigatus Cyclophilin reveals 3D Domain Swapping of a Central Element
ComponentsPPIASEProlyl isomerase
KeywordsISOMERASE / 3D DOMAIN SWAPPING / MISFOLDING / PPIASE / ASP F 11 / ALLERGEN / ROTAMASE
Function / homology
Function and homology information


cyclosporin A binding / protein peptidyl-prolyl isomerization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / identical protein binding / 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
Peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsLimacher, A. / Kloer, D.P. / Fluckiger, S. / Folkers, G. / Crameri, R. / Scapozza, L.
CitationJournal: Structure / Year: 2006
Title: The Crystal Structure of Aspergillus Fumigatus Cyclophilin Reveals 3D Domain Swapping of a Central Element
Authors: Limacher, A. / Kloer, D.P. / Fluckiger, S. / Folkers, G. / Crameri, R. / Scapozza, L.
History
DepositionOct 5, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PPIASE
B: PPIASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9894
Polymers37,7962
Non-polymers1922
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.829, 64.829, 156.288
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein PPIASE / Prolyl isomerase / CYCLOPHILIN


Mass: 18898.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Plasmid: PQE32 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: Q9Y7F6, UniProt: Q4WHY9*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.93 Å3/Da / Density % sol: 57.75 %
Crystal growpH: 6
Details: DROP SOLUTION: 13% AMMONIUM SULFATE, 0.1 M MES PH 6. RESERVOIR SOLUTION: 50% AMMONIUM SULFATE, 0.1 M SODIUM CITRATE PH 5.5.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.85→45.6 Å / Num. obs: 33079 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.2
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→55.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.037 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1675 5.1 %RANDOM
Rwork0.189 ---
obs0.191 31360 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.85→55.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 10 123 2295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222224
X-RAY DIFFRACTIONr_bond_other_d0.0010.022018
X-RAY DIFFRACTIONr_angle_refined_deg1.9471.9442989
X-RAY DIFFRACTIONr_angle_other_deg0.93234704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.095271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84323.36798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.60215398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.021516
X-RAY DIFFRACTIONr_chiral_restr0.1190.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
X-RAY DIFFRACTIONr_nbd_refined0.1980.2382
X-RAY DIFFRACTIONr_nbd_other0.1780.21928
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21070
X-RAY DIFFRACTIONr_nbtor_other0.0850.21326
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.941.51766
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3322216
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.5293998
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.1874.5773
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.288 136
Rwork0.24 2264
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.00141.72920.31433.99541.43012.4284-0.22460.48850.2039-0.690.15880.2555-0.2537-0.12620.0658-0.0108-0.05110.0008-0.14720.0205-0.170724.2957-3.988574.4592
26.44290.24410.08195.98441.59137.2573-0.09370.43420.0639-0.36030.10320.5598-0.1177-0.438-0.0094-0.12770.08140.0171-0.2162-0.0357-0.089520.81096.214695.1479
34.0487-2.0089-0.13963.98110.362.7609-0.2021-0.4112-0.1790.52470.17490.33940.2408-0.08820.0273-0.0380.09410.0591-0.18330.0131-0.140525.18912.1288107.0887
49.04482.8201-0.9565.71694.255813.0616-0.0677-0.13290.05060.1294-0.01270.74590.0744-0.44820.0804-0.1361-0.02460.024-0.2265-0.0346-0.084418.7833-4.492684.2331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 69
2X-RAY DIFFRACTION1A128 - 171
3X-RAY DIFFRACTION2A92 - 127
4X-RAY DIFFRACTION3B1 - 68
5X-RAY DIFFRACTION3B128 - 171
6X-RAY DIFFRACTION4B96 - 127

+
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