[English] 日本語
Yorodumi
- PDB-7cyy: Crystal structure of Arabinose isomerase from hybrid AI8 with Adonitol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cyy
TitleCrystal structure of Arabinose isomerase from hybrid AI8 with Adonitol
ComponentsL-arabinose isomerase
KeywordsISOMERASE / hybrid / Arabinose isomerase
Function / homology
Function and homology information


L-arabinose isomerase / L-arabinose isomerase activity / L-arabinose catabolic process to D-xylulose 5-phosphate / manganese ion binding / cytosol
Similarity search - Function
: / : / L-arabinose isomerase central domain / L-arabinose isomerase / L-arabinose isomerase, C-terminal / L-arabinose isomerase, N-terminal domain superfamily / L-arabinose isomerase N-terminal domain / L-arabinose isomerase C-terminal domain / L-fucose/L-arabinose isomerase, C-terminal / L-fucose isomerase, N-terminal/central domain superfamily
Similarity search - Domain/homology
: / D-ribitol / L-arabinose isomerase / L-arabinose isomerase / L-arabinose isomerase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
Alicyclobacillus sp. TP-7 (bacteria)
Alicyclobacillus acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHoang, N.K.Q. / Dhanasingh, I. / Cao, T.P. / Sung, J.Y. / Shin, S.M. / Lee, D.W. / Lee, S.H.
CitationJournal: To Be Published
Title: Crystal structure of Arabinose isomerase from hyper thermophilic hybrid AI8 with Adonitol
Authors: Hoang, N.K.Q. / Dhanasingh, I. / Cao, T.P. / Sung, J.Y. / Shin, S.M. / Lee, D.W. / Lee, S.H.
History
DepositionSep 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase
D: L-arabinose isomerase
E: L-arabinose isomerase
F: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,32923
Polymers335,6866
Non-polymers1,64417
Water4,450247
1
A: L-arabinose isomerase
B: L-arabinose isomerase
D: L-arabinose isomerase
E: L-arabinose isomerase
hetero molecules

C: L-arabinose isomerase
F: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,32923
Polymers335,6866
Non-polymers1,64417
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area42220 Å2
ΔGint-223 kcal/mol
Surface area83730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.582, 82.120, 192.726
Angle α, β, γ (deg.)90.000, 117.930, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
L-arabinose isomerase


Mass: 55947.586 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Chimeric protein
Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria), (gene. exp.) Alicyclobacillus sp. TP-7 (bacteria), (gene. exp.) Alicyclobacillus acidocaldarius (bacteria)
Gene: araA, GK1904, araA / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q5KYP7, UniProt: K0IGW6, UniProt: Q2VMT2, L-arabinose isomerase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-RB0 / D-ribitol


Mass: 152.146 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H12O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 35% (v/v) MPD, 100mM Imidazole/ Hydrochloric acid pH 8.0, 200mM Magnesium chloride

-
Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 88026 / % possible obs: 99 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.081 / Rrim(I) all: 0.212 / Χ2: 1.066 / Net I/σ(I): 3.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.646.10.99744090.6360.4341.090.51998.7
2.64-2.6960.8942270.6890.3880.9730.49996.8
2.69-2.746.80.79543600.7510.330.8620.5399.7
2.74-2.86.90.73444190.7970.3010.7940.55599.7
2.8-2.866.90.63844110.8350.2620.6910.59699.5
2.86-2.936.90.56844200.850.2320.6140.62499.7
2.93-36.90.49843830.8870.2050.5390.68299.5
3-3.086.70.4343740.9010.1790.4670.799.3
3.08-3.176.60.36544290.9240.1520.3960.81699.3
3.17-3.286.20.31943160.9240.1380.3490.87797.8
3.28-3.396.70.25443720.9580.1050.2750.93898.8
3.39-3.536.90.22844030.9670.0940.2471.07799.7
3.53-3.696.90.20144160.9720.0830.2181.18699.7
3.69-3.886.80.17844090.9760.0730.1931.34699.7
3.88-4.136.70.16244670.980.0680.1761.47499.2
4.13-4.456.30.14443160.9820.0620.1571.6297.7
4.45-4.8970.13344570.9870.0540.1441.73399.5
4.89-5.66.80.13344430.9850.0550.1441.57299.4
5.6-7.056.40.1344370.9830.0550.1411.52498.3
7.05-506.40.10645580.9910.0460.1162.39698.9

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AJT

2ajt


Resolution: 2.6→48.18 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 4497 5.12 %RANDOM
Rwork0.1865 83415 --
obs0.1903 87912 98.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.27 Å2 / Biso mean: 50.9613 Å2 / Biso min: 22.91 Å2
Refinement stepCycle: final / Resolution: 2.6→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23444 0 85 247 23776
Biso mean--65.6 44.72 -
Num. residues----2962
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.58-2.610.3581040.27632169227377
2.61-2.640.3081720.25812766293898
2.64-2.670.32881470.24162656280396
2.67-2.710.31381360.22442836297299
2.71-2.740.3451490.224428312980100
2.74-2.780.32211430.22627832926100
2.78-2.820.3061300.23672813294399
2.82-2.860.34371470.241628192966100
2.86-2.910.32741370.241828572994100
2.91-2.960.30541410.245127482889100
2.96-3.010.35041360.25762824296099
3.01-3.060.32241640.24622791295599
3.06-3.120.30991550.22952777293299
3.12-3.180.31381730.22042788296199
3.18-3.250.29771670.20962761292898
3.25-3.330.28911450.19522755290098
3.33-3.410.26271380.197128262964100
3.41-3.50.31891470.191928002947100
3.5-3.610.28371440.188128512995100
3.61-3.720.25931710.176728212992100
3.72-3.860.24311620.172759292199
3.86-4.010.25531740.16452803297799
4.01-4.190.22121530.15972820297399
4.19-4.410.21771540.15542737289197
4.41-4.690.22181600.14332838299899
4.69-5.050.22391720.15042806297899
5.05-5.560.22941420.16372853299599
5.56-6.360.24251470.18132807295498
6.36-8.010.22341560.16292852300899
8.01-48.180.19411310.17132868299996

+
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