[English] 日本語
Yorodumi
- PDB-2p05: Structural Insights into the Evolution of a Non-Biological Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2p05
TitleStructural Insights into the Evolution of a Non-Biological Protein
Componentsa non-biological ATP binding protein 1819
KeywordsDE NOVO PROTEIN / alpha/beta fold
Function / homologyNuclear Transport Factor 2; Chain: A, - #210 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / ADENOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsSmith, M. / Rosenow, M. / Wang, M. / Allen, J.P. / Szostak, J.W. / Chaput, J.C.
CitationJournal: PLoS ONE / Year: 2007
Title: Structural insights into the evolution of a non-biological protein: importance of surface residues in protein fold optimization.
Authors: Smith, M.D. / Rosenow, M.A. / Wang, M. / Allen, J.P. / Szostak, J.W. / Chaput, J.C.
History
DepositionFeb 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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: a non-biological ATP binding protein 1819
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4895
Polymers9,7231
Non-polymers7664
Water00
1
A: a non-biological ATP binding protein 1819
hetero molecules

A: a non-biological ATP binding protein 1819
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,97910
Polymers19,4462
Non-polymers1,5338
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3430 Å2
ΔGint-54 kcal/mol
Surface area8620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.460, 71.460, 55.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-300-

CL

-
Components

#1: Protein a non-biological ATP binding protein 1819


Mass: 9723.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.19 Å3/Da / Density % sol: 70.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 250 mM sodium citrate, 100 mM sodium phosphate, 10 mM ATP, 300 mM sodium chloride, and 0.4-0.8% x/v polyethylene glycol 400, pH 8.5, VAPOR DIFFUSION, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.2830, 1.2834, 1.2398
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.2831
21.28341
31.23981
Reflection

D res high: 2.8 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsRsym valueD res low (Å)Num. obs% possible obs
4.516.6191670.0990.09961.8984235100
4.324.2178810.1370.13761.663418499.9
3.934.4167410.1390.13962.017425999.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.8561.999.910.0310.0314
6.268.8510010.0420.0424.4
5.116.2699.510.0620.0624.1
4.435.1110010.0610.0614.4
3.964.4310010.0660.0664.5
3.613.9610010.0870.0874.6
3.353.6110010.1310.1314.6
3.133.3510010.1810.1814.6
2.953.1310010.2870.2874.7
2.82.9510010.4420.4424.7
8.8561.6699.520.0930.0933.7
6.268.8510020.0980.0984.3
5.116.2699.520.1020.1023.9
4.435.1110020.0990.0994.1
3.964.4310020.1040.1044.2
3.613.9610020.1280.1284.3
3.353.6110020.160.164.3
3.133.3510020.2030.2034.4
2.953.1310020.2860.2864.4
2.82.9510020.4040.4044.4
8.8562.0299.530.0690.0693.4
6.268.8510030.080.083.9
5.116.2699.130.10.13.6
4.435.1110030.10.13.9
3.964.4310030.1010.1013.9
3.613.9610030.1260.1263.9
3.353.6110030.1640.1644
3.133.3510030.2230.2234
2.953.1310030.3490.3494.1
2.82.9510030.4970.4974
ReflectionResolution: 2.8→61.898 Å / Num. obs: 4235 / % possible obs: 100 % / Redundancy: 4.5 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.8-2.954.70.4421.628176030.442100
2.95-3.134.70.2872.526845750.287100
3.13-3.354.60.181425105410.181100
3.35-3.614.60.1315.422884950.131100
3.61-3.964.60.087821704740.087100
3.96-4.434.50.0668.718664160.066100
4.43-5.114.40.06110.617083870.061100
5.11-6.264.10.0621113313220.06299.5
6.26-8.854.40.04216.811612620.042100
8.85-61.940.03120.36321600.03199.9

-
Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength11.2834.8-7.11
13 wavelength21.23983.98-3.17
13 wavelength31.28343.3-9.25

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.8→61.898 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.852 / SU B: 12.638 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.397 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.296 192 4.5 %RANDOM
Rwork0.238 ---
obs0.241 4222 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.084 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20.96 Å20 Å2
2--1.92 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.8→61.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms538 0 45 0 583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021597
X-RAY DIFFRACTIONr_angle_refined_deg2.1391.991803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.997562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25722.22227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.30215105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.987155
X-RAY DIFFRACTIONr_chiral_restr0.1440.279
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02423
X-RAY DIFFRACTIONr_nbd_refined0.2550.2246
X-RAY DIFFRACTIONr_nbtor_refined0.3270.2390
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.214
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.24
X-RAY DIFFRACTIONr_mcbond_it1.2861.5324
X-RAY DIFFRACTIONr_mcangle_it2.2612510
X-RAY DIFFRACTIONr_scbond_it2.5653334
X-RAY DIFFRACTIONr_scangle_it4.0564.5293
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 20 -
Rwork0.304 283 -
obs-303 100 %

+
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://pdbjlvh1.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