[English] 日本語
Yorodumi
- PDB-4p81: Structure of ancestral PyrR protein (AncORANGEPyrR) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p81
TitleStructure of ancestral PyrR protein (AncORANGEPyrR)
ComponentsAncestral PyrR protein (Orange)
KeywordsTRANSCRIPTION / RNA binding proteins / reconstructed amino acid sequence
Function / homologyRossmann fold - #2020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPerica, T. / Kondo, Y. / Tiwari, S. / McLaughlin, S. / Steward, A. / Reuter, N. / Clarke, J. / Teichmann, S.A.
CitationJournal: Science / Year: 2014
Title: Evolution of oligomeric state through allosteric pathways that mimic ligand binding.
Authors: Perica, T. / Kondo, Y. / Tiwari, S.P. / McLaughlin, S.H. / Kemplen, K.R. / Zhang, X. / Steward, A. / Reuter, N. / Clarke, J. / Teichmann, S.A.
History
DepositionMar 29, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ancestral PyrR protein (Orange)
B: Ancestral PyrR protein (Orange)
C: Ancestral PyrR protein (Orange)
D: Ancestral PyrR protein (Orange)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9899
Polymers80,5134
Non-polymers4765
Water6,882382
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-99 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.910, 102.300, 107.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULYSLYSAA4 - 1804 - 180
21GLUGLULYSLYSBB4 - 1804 - 180
12GLUGLUGLUGLUAA4 - 1794 - 179
22GLUGLUGLUGLUCC4 - 1794 - 179
13GLUGLUGLUGLUAA4 - 1794 - 179
23GLUGLUGLUGLUDD4 - 1794 - 179
14GLNGLNGLUGLUBB3 - 1793 - 179
24GLNGLNGLUGLUCC3 - 1793 - 179
15GLNGLNLYSLYSBB3 - 1803 - 180
25GLNGLNLYSLYSDD3 - 1803 - 180
16SERSERGLUGLUCC2 - 1792 - 179
26SERSERGLUGLUDD2 - 1792 - 179

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Ancestral PyrR protein (Orange)


Mass: 20128.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG-300, 10% glycerol, 0.1M Tris pH 8.5, 5% PEG-8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→38.9 Å / Num. obs: 55721 / % possible obs: 94.8 % / Redundancy: 3.7 % / Net I/σ(I): 7.6
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 1.6 / % possible all: 96

-
Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a3c

1a3c


Resolution: 1.8→74.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.1 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22378 2914 5 %RANDOM
Rwork0.18174 ---
obs0.18378 55721 94.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.087 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---0.19 Å20 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.8→74.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 0 26 382 5652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195384
X-RAY DIFFRACTIONr_bond_other_d0.0110.025546
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.9987264
X-RAY DIFFRACTIONr_angle_other_deg1.662312713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0655672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60323.278241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.854151061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2341567
X-RAY DIFFRACTIONr_chiral_restr0.1090.2873
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025945
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021110
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6022.4382694
X-RAY DIFFRACTIONr_mcbond_other2.5992.4382693
X-RAY DIFFRACTIONr_mcangle_it3.4983.633364
X-RAY DIFFRACTIONr_mcangle_other3.4983.6313365
X-RAY DIFFRACTIONr_scbond_it4.0492.9932690
X-RAY DIFFRACTIONr_scbond_other4.0492.9932690
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0334.2773901
X-RAY DIFFRACTIONr_long_range_B_refined7.47424.03722543
X-RAY DIFFRACTIONr_long_range_B_other7.47424.03722542
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A109910.12
12B109910.12
21A104210.12
22C104210.12
31A106130.13
32D106130.13
41B105670.12
42C105670.12
51B107930.13
52D107930.13
61C104690.12
62D104690.12
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 207 -
Rwork0.288 4122 -
obs--95.94 %

+
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