[English] 日本語
Yorodumi
- PDB-1n0r: 4ANK: A designed ankyrin repeat protein with four identical conse... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n0r
Title4ANK: A designed ankyrin repeat protein with four identical consensus repeats
Components4 ankyrin repeats
KeywordsSTRUCTURAL PROTEIN / ANKYRIN REPEAT / ANK
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / BROMIDE ION
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Single anomolous diffraction / Resolution: 1.5 Å
AuthorsMosavi, L.K. / Minor Jr., D.L. / Peng, Z.-Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Consensus-derived structural determinants of the ankyrin repeat motif.
Authors: Mosavi, L.K. / Minor Jr., D.L. / Peng, Z.-Y.
History
DepositionOct 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Database references / Structure summary
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4 ankyrin repeats
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6083
Polymers13,4481
Non-polymers1602
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.429, 46.115, 81.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 4 ankyrin repeats / 4ANK


Mass: 13448.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Gene: designed consensus ankyrin repeat / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: sodium cacodylate, magnesium bromide, MPD, isopropanol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein1drop
20.2 M1reservoirMgBr2
30.1 Msodium cacodylate1reservoirpH6.4
433 %MPD1reservoir
515 %isopropanol1reservoir

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9199 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 29, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9199 Å / Relative weight: 1
ReflectionResolution: 1.5→46.14 Å / Num. all: 17879 / Num. obs: 16966 / % possible obs: 99.78 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.07
Reflection
*PLUS
Highest resolution: 1.5 Å / % possible obs: 99.92 % / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Num. unique obs: 913 / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.7

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: Single anomolous diffraction / Resolution: 1.5→19.65 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.524 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24916 913 5.1 %RANDOM
Rwork0.21605 ---
all0.21605 ---
obs0.21763 16966 99.92 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.619 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 2 86 1034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021958
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9771295
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4923125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11415174
X-RAY DIFFRACTIONr_chiral_restr0.0940.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02712
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2460.3481
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.566
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.324
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7150.521
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8181.5621
X-RAY DIFFRACTIONr_mcangle_it1.5282977
X-RAY DIFFRACTIONr_scbond_it3.1733337
X-RAY DIFFRACTIONr_scangle_it4.8184.5318
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.351 59
Rwork0.247 1229
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)
10.24140.36210.25440.59320.48512.5717-0.0113-0.03510.0335-0.0048-0.07550.0865-0.0098-0.12020.08670.08470.0022-0.00230.1027-0.00720.117521.059643.233118.1339
2-35.9116-7.368510.3643-25.2849-10.0884-1.99590.1039-0.66350.02830.3252-0.1365-0.29730.02070.05720.03260.11580.0086-0.03660.1150.04250.029529.757743.572725.0751
30.19910.0612-0.41320.98150.86593.0496-0.04420.01630.0468-0.0377-0.09310.0539-0.0031-0.20040.13720.0217-0.0214-0.00930.06210.02580.130522.541441.298814.9966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1261 - 126
2X-RAY DIFFRACTION2AB - C127 - 1281 - 2
3X-RAY DIFFRACTION3AD129 - 2141 - 86
Refinement
*PLUS
Rfactor Rfree: 0.249 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.49

+
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://pdbjlc1.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