[English] 日本語
Yorodumi
- PDB-1oz9: Crystal structure of AQ_1354, a hypothetical protein from Aquifex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1oz9
TitleCrystal structure of AQ_1354, a hypothetical protein from Aquifex aeolicus
ComponentsHypothetical protein AQ_1354Hypothesis
KeywordsUNKNOWN FUNCTION / matrix metalloproteinase type fold / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


RNA endonuclease activity / metalloendopeptidase activity / rRNA processing / Hydrolases; Acting on ester bonds / zinc ion binding / cytoplasm
Similarity search - Function
Metalloproteases ("zincins"), catalytic domain / Endoribonuclease YbeY, conserved site / Uncharacterized protein family UPF0054 signature. / Endoribonuclease YbeY / Metalloprotease catalytic domain superfamily, predicted / Endoribonuclease YbeY / Collagenase (Catalytic Domain) / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Endoribonuclease YbeY
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.894 Å
AuthorsOganesyan, V. / Busso, D. / Brandsen, J. / Chen, S. / Jancarik, J. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of the hypothetical protein AQ_1354 from Aquifex aeolicus.
Authors: Oganesyan, V. / Busso, D. / Brandsen, J. / Chen, S. / Jancarik, J. / Kim, R. / Kim, S.H.
History
DepositionApr 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein AQ_1354


Theoretical massNumber of molelcules
Total (without water)17,3721
Polymers17,3721
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.018, 58.018, 110.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a monomer

-
Components

#1: Protein Hypothetical protein AQ_1354 / Hypothesis


Mass: 17372.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pLIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O67367
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.76 Å3/Da / Density % sol: 55.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4K, Na Acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
220 mMTris-HCl1droppH7.0
310 mM1dropNaCl
41 mMdithiothreitol1drop
51 mMEDTA1drop
6200 mMsodium acetate1reservoir
7100 mMTris-HCl1reservoirpH8.5
830 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 14, 2002 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.89→41.17 Å / Num. all: 14413 / Num. obs: 14413 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 25
Reflection shellResolution: 1.894→1.943 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.2 / Num. unique all: 982 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 41.2 Å / Num. obs: 28054 / % possible obs: 96.3 % / Redundancy: 9.3 %
Reflection shell
*PLUS
Highest resolution: 1.89 Å / Lowest resolution: 1.97 Å / % possible obs: 85.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.25

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.894→12 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.105 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.151 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23423 712 5 %RANDOM
Rwork0.20524 ---
all0.21522 ---
obs0.20658 13420 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.133 Å0.146 Å
Refinement stepCycle: LAST / Resolution: 1.894→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 0 0 50 1201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211166
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9871558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5983140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.53415247
X-RAY DIFFRACTIONr_chiral_restr0.1060.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02844
X-RAY DIFFRACTIONr_nbd_refined0.2130.3479
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.583
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3050.329
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5320.520
X-RAY DIFFRACTIONr_mcbond_it0.7811.5696
X-RAY DIFFRACTIONr_mcangle_it1.50421119
X-RAY DIFFRACTIONr_scbond_it2.6553470
X-RAY DIFFRACTIONr_scangle_it4.5274.5439
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 48 -
Rwork0.22 939 -
obs-982 82 %
Refinement TLS params.Method: refined / Origin x: 47.99 Å / Origin y: 18.021 Å / Origin z: 43.601 Å
111213212223313233
T0.1014 Å2-0.0123 Å2-0.0396 Å2-0.0064 Å2-0.0086 Å2--0.0522 Å2
L2.8889 °2-0.7968 °21.4808 °2-3.9555 °2-0.2594 °2--3.0802 °2
S0.0887 Å °-0.0857 Å °0.0419 Å °0.1687 Å °-0.0634 Å °-0.2591 Å °0.0133 Å °0.1127 Å °-0.0253 Å °
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.89 Å / Num. reflection obs: 15227 / % reflection Rfree: 5 % / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.524

+
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