[English] 日本語
Yorodumi
- PDB-3bqb: Hexagonal kristal form of 2-keto-3-deoxyarabinonate dehydratase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bqb
TitleHexagonal kristal form of 2-keto-3-deoxyarabinonate dehydratase
ComponentsPutative uncharacterized protein
KeywordsLYASE / FAH-family fold
Function / homology
Function and homology information


2-dehydro-3-deoxy-D-arabinonate dehydratase / D-arabinose catabolic process / hydro-lyase activity / protein homotetramerization / magnesium ion binding
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #40 / : / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetate (FAA) hydrolase C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Vcp-like ATPase; Chain A, domain 2 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2-dehydro-3-deoxy-D-arabinonate dehydratase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBarends, T.M. / Brouns, S. / Worm, P. / Akerboom, J. / Turnbull, A. / Salmon, L.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily
Authors: Brouns, S.J.J. / Barends, T.R.M. / Worm, P. / Akerboom, J. / Turnbull, A.P. / Salmon, L. / van der Oost, J.
History
DepositionDec 20, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative uncharacterized protein
X: Putative uncharacterized protein
Z: Putative uncharacterized protein
Y: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,8388
Polymers132,7404
Non-polymers974
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Putative uncharacterized protein
X: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4194
Polymers66,3702
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-28 kcal/mol
Surface area23220 Å2
MethodPISA
3
Z: Putative uncharacterized protein
Y: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4194
Polymers66,3702
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-26 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.092, 157.092, 131.921
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein
Putative uncharacterized protein / 2-keto-3-deoxyarabinonate dehydratase


Mass: 33185.078 Da / Num. of mol.: 4 / Fragment: UNP residues 6-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: DKAD / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q97UA0
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.54 Å3/Da / Density % sol: 65.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: Na/K-phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 7, 2005 / Details: Osmic mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→99.9 Å / Num. all: 50804 / Num. obs: 50804 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 81.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 30.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 3.4 / Num. unique all: 5043 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q18

2q18


Resolution: 2.7→33.74 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 13.219 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.578 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28355 2562 5.1 %RANDOM
Rwork0.23808 ---
all0.24031 48004 --
obs0.24031 48004 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 63.124 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20.95 Å20 Å2
2--1.89 Å20 Å2
3----2.84 Å2
Refinement stepCycle: LAST / Resolution: 2.7→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9024 0 4 56 9084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229182
X-RAY DIFFRACTIONr_bond_other_d0.0010.028662
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.98812430
X-RAY DIFFRACTIONr_angle_other_deg0.709320182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7951130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12823.945398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.195151697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9881574
X-RAY DIFFRACTIONr_chiral_restr0.0580.21429
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029992
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021762
X-RAY DIFFRACTIONr_nbd_refined0.180.21671
X-RAY DIFFRACTIONr_nbd_other0.1620.29265
X-RAY DIFFRACTIONr_nbtor_refined0.1650.24534
X-RAY DIFFRACTIONr_nbtor_other0.0750.25543
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2227
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1730.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0430.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5151.57484
X-RAY DIFFRACTIONr_mcbond_other0.0351.52294
X-RAY DIFFRACTIONr_mcangle_it0.54629270
X-RAY DIFFRACTIONr_scbond_it0.45134095
X-RAY DIFFRACTIONr_scangle_it0.7084.53160
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.696→2.766 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 197 -
Rwork0.389 3377 -
obs--95.51 %

+
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