[English] 日本語
Yorodumi
- PDB-1t3u: Unknown conserved bacterial protein from Pseudomonas aeruginosa PAO1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t3u
TitleUnknown conserved bacterial protein from Pseudomonas aeruginosa PAO1
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / T1445 / NYSGXRC / UNKNOWN ORF / COG3027 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


septin ring assembly / cell septum / FtsZ-dependent cytokinesis / division septum assembly / cell division site / cytosol
Similarity search - Function
Cell division protein ZapA, N-terminal / Cell division protein ZapA protomer, N-terminal domain / Cell division protein ZapA-like / Cell division protein ZapA-like superfamily / Cell division protein ZapA / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Double Stranded RNA Binding Domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich ...Cell division protein ZapA, N-terminal / Cell division protein ZapA protomer, N-terminal domain / Cell division protein ZapA-like / Cell division protein ZapA-like superfamily / Cell division protein ZapA / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Double Stranded RNA Binding Domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cell division protein ZapA
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsRajashankar, K.R. / Kneiwel, R. / Solorzano, V. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structure of a conserved hypothetical protein Pseudomonas aeruginosa PA01
Authors: Rajashankar, K.R. / Kneiwel, R. / Solorzano, V. / Lima, C.D.
History
DepositionApr 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 300THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). THE ...THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). THE BIOLOGICAL MOLECULE IS REPRESENTED AS A TETRAMER IN THE ASYMMETRIC UNIT, HOWEVER THE PHYSIOLOGICAL STATE OF THE PROTEIN IS NOT KNOWN YET.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: conserved hypothetical protein
B: conserved hypothetical protein
C: conserved hypothetical protein
D: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)47,0684
Polymers47,0684
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-78 kcal/mol
Surface area21460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.726, 106.726, 36.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsUNKNOWN, BUT TETRAMER IN THE ASYMMETRIC UNIT COULD BE THE PHYSIOLOGICAL OLIGOMER DUE TO CONTACTS AND A SYMMETRY

-
Components

#1: Protein
conserved hypothetical protein


Mass: 11766.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PA01 / Gene: PA5227 / Plasmid: T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: Q9HTW3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.16 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M SODIUM CITRATE, 17% ISOPROPANOL, 9% PEG 4K, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 31, 2003 / Details: mirrors
RadiationMonochromator: DIAMOND / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 31182 / Num. obs: 28501 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 58 Å2 / Rsym value: 0.055 / Net I/σ(I): 11
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 1.75 / Rsym value: 0.241 / % possible all: 79

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 322107.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1222 4.7 %RANDOM
Rwork0.236 ---
obs0.236 25837 92.9 %-
all-27812 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.7363 Å2 / ksol: 0.328184 e/Å3
Displacement parametersBiso mean: 53.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å20 Å2
2--2.09 Å20 Å2
3----4.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-6 Å
Luzzati sigma a0.41 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 0 48 2975
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.692
X-RAY DIFFRACTIONc_scbond_it2.632
X-RAY DIFFRACTIONc_scangle_it4.092.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 201 5.2 %
Rwork0.316 3688 -
obs--83.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

+
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