[English] 日本語
Yorodumi
- PDB-1x8f: Crystal Structure Of apo-Kdo8P Synthase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1x8f
TitleCrystal Structure Of apo-Kdo8P Synthase
Components2-dehydro-3-deoxyphosphooctonate aldolase
KeywordsTRANSFERASE / BETA-ALPHA-BARRELS / LYASE / LIPOPOLYSACCHARIDE
Function / homology
Function and homology information


3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
3-deoxy-8-phosphooctulonate synthase / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVainer, R. / Belakhov, V. / Rabkin, E. / Baasov, T. / Adir, N.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structures of Escherichia coli KDO8P Synthase Complexes Reveal the Source of Catalytic Irreversibility
Authors: Vainer, R. / Belakhov, V. / Rabkin, E. / Baasov, T. / Adir, N.
History
DepositionAug 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-dehydro-3-deoxyphosphooctonate aldolase


Theoretical massNumber of molelcules
Total (without water)30,8711
Polymers30,8711
Non-polymers00
Water82946
1
A: 2-dehydro-3-deoxyphosphooctonate aldolase

A: 2-dehydro-3-deoxyphosphooctonate aldolase

A: 2-dehydro-3-deoxyphosphooctonate aldolase

A: 2-dehydro-3-deoxyphosphooctonate aldolase


Theoretical massNumber of molelcules
Total (without water)123,4834
Polymers123,4834
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_657-x+1,y,-z+21
crystal symmetry operation4_567x,-y+1,-z+21
Buried area13540 Å2
ΔGint-83 kcal/mol
Surface area38910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)118.681, 118.681, 118.681
Angle α, β, γ (deg.)90, 90, 90
Int Tables number197
Space group name H-MI23
DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: X,Y,Z -X,-Y,Z -X,Y,-Z X,-Y,-Z Z,X,Y Z,-X,-Y -Z,-X,Y -Z,X,-Y Y,Z,X -Y,Z,-X Y,-Z,-X -Y,-Z,X 1/2+X,1/2+Y,1/2+Z 1/2-X,1/2-Y,1/2+Z 1/2-X,1/2+Y,1/2-Z 1/2+X,1/2-Y,1/2-Z 1/2+Z,1/2+X,1/2+Y 1/2+Z,1/2-X,1/2-Y 1/2-Z,1/2-X,1/2+Y 1/2-Z,1/2+X,1/2-Y 1/2+Y,1/2+Z,1/2+X 1/2-Y,1/2+Z,1/2-X 1/2+Y,1/2-Z,1/2-X 1/2-Y,1/2-Z,1/2+X

-
Components

#1: Protein 2-dehydro-3-deoxyphosphooctonate aldolase / Phospho-2-dehydro-3-deoxyoctonate aldolase / 3-deoxy-D-manno-octulosonic acid 8-phosphate ...Phospho-2-dehydro-3-deoxyoctonate aldolase / 3-deoxy-D-manno-octulosonic acid 8-phosphate synthetase / KDO-8-phosphate synthetase / KDO 8-P synthase / KDOPS


Mass: 30870.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kdsA / Plasmid: pJU1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: P0A715, 3-deoxy-8-phosphooctulonate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.2 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, tris-HCl, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 10401 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.1
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.45 / Num. unique all: 647 / % possible all: 100

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PHW

1phw


Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.255 940 random
Rwork0.239 --
all0.243 9001 -
obs0.239 8061 -
Displacement parametersBiso mean: 72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 0 46 2128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0105
X-RAY DIFFRACTIONc_angle_d1.62
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d1.45

+
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