[English] 日本語
Yorodumi
- PDB-2rfm: Structure of a Thermophilic Ankyrin Repeat Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rfm
TitleStructure of a Thermophilic Ankyrin Repeat Protein
ComponentsPutative ankyrin repeat protein TV1425
KeywordsPROTEIN BINDING / Ankyrin Repeat / ANK repeat
Function / homology
Function and homology information


Ankyrin repeats (many copies) / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / 1,3-BUTANEDIOL / Putative ankyrin repeat protein TV1425
Similarity search - Component
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsLoew, C. / Weininger, U. / Neumann, P. / Stubbs, M.T. / Balbach, J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural insights into an equilibrium folding intermediate of an archaeal ankyrin repeat protein
Authors: Loew, C. / Weininger, U. / Neumann, P. / Klepsch, M. / Lilie, H. / Stubbs, M.T. / Balbach, J.
History
DepositionOct 1, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Putative ankyrin repeat protein TV1425
B: Putative ankyrin repeat protein TV1425
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,15524
Polymers43,2452
Non-polymers1,91022
Water8,629479
1
A: Putative ankyrin repeat protein TV1425
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,58611
Polymers21,6231
Non-polymers96310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative ankyrin repeat protein TV1425
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,57013
Polymers21,6231
Non-polymers94712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Putative ankyrin repeat protein TV1425
B: Putative ankyrin repeat protein TV1425
hetero molecules

A: Putative ankyrin repeat protein TV1425
B: Putative ankyrin repeat protein TV1425
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,31148
Polymers86,4914
Non-polymers3,82044
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area12960 Å2
ΔGint-208.6 kcal/mol
Surface area31270 Å2
MethodPISA
4
A: Putative ankyrin repeat protein TV1425
hetero molecules

B: Putative ankyrin repeat protein TV1425
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,15524
Polymers43,2452
Non-polymers1,91022
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation11_655-x+y+1,y,-z1
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-99.3 kcal/mol
Surface area18000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.002, 101.002, 174.483
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

21B-415-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Putative ankyrin repeat protein TV1425


Mass: 21622.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium (archaea) / Gene: TVG1472127 / Plasmid: pet28c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q978J0

-
Non-polymers , 6 types, 501 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#4: Chemical
ChemComp-BU2 / 1,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% Glycerol, 2M Ammoniumsulfate, 1% 1,3-butanediole, 20mM HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 286K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11801
21801
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONBESSY 14.210.9238
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDJul 12, 2006
RIGAKU2IMAGE PLATEFeb 12, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.92381
21.54181
ReflectionRedundancy: 15.4 % / Av σ(I) over netI: 5.4 / Number: 715122 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / D res high: 1.83 Å / D res low: 174.483 Å / Num. obs: 46388 / % possible obs: 98.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.7930.9299.410.0710.07115.9
4.095.7910010.0710.07117.3
3.344.0910010.0660.06617.6
2.893.3410010.0730.07317.7
2.592.8910010.0880.08817.6
2.362.5910010.1040.10417.7
2.192.3610010.130.1317.6
2.052.1910010.1650.16517.5
1.932.0599.810.2110.21112
1.831.9389.910.3120.3127.2
ReflectionResolution: 1.65→48.472 Å / Num. obs: 58965 / % possible obs: 93 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 9.9 % / Biso Wilson estimate: 19.96 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.65-1.746.20.3232.43742460520.35366.9
1.74-1.847.50.2223.45441272730.22285.2
1.84-1.9710.20.1593.38245680840.15999.5
1.97-2.13110.0937.78340175480.09399.7
2.13-2.33110.06310.47719769920.06399.8
2.33-2.61110.05212.87025963800.05299.9
2.61-3.0110.90.03916.36199256660.039100
3.01-3.6910.90.04511.85268248550.045100
3.69-5.2210.60.0559.64085138450.055100
5.22-61.669.80.02719.92218222700.02799.5

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.349 / SU ML: 0.043 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.081 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS refinement - 1 group for every molecule.
RfactorNum. reflection% reflectionSelection details
Rfree0.178 3022 5.1 %RANDOM
Rwork0.156 ---
all0.15695 ---
obs0.157 58909 92.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.827 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0.12 Å20 Å2
2---0.24 Å20 Å2
3---0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.079 Å0.081 Å
Luzzati d res low-8 Å
Luzzati sigma a0.043 Å0 Å
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 111 479 3499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223285
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9994438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5925419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34524.932146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03415619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5911522
X-RAY DIFFRACTIONr_chiral_restr0.10.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022416
X-RAY DIFFRACTIONr_nbd_refined0.2450.31863
X-RAY DIFFRACTIONr_nbtor_refined0.3220.52351
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.5712
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.363
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.559
X-RAY DIFFRACTIONr_mcbond_it1.1722045
X-RAY DIFFRACTIONr_mcangle_it1.75433223
X-RAY DIFFRACTIONr_scbond_it1.60521381
X-RAY DIFFRACTIONr_scangle_it2.34231215
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 148 -
Rwork0.156 2737 -
all-2885 -
obs--62.83 %
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)
10.94050.0322-0.31630.9245-0.02810.68470.0028-0.01080.05670.00730.0009-0.0084-0.00710.0176-0.0036-0.35590.02050.0041-0.2802-0.0044-0.379538.27642.74815.737
21.52340.0736-0.03290.9276-0.03760.5035-0.0187-0.1193-0.21720.0614-0.0238-0.08490.08030.08080.0425-0.34070.0140.0171-0.20960.012-0.345863.0634.22413.468
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 18810 - 191
2X-RAY DIFFRACTION2BB6 - 1899 - 192

+
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