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- PDB-1d9e: STRUCTURE OF E. COLI KDO8P SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1d9e
TitleSTRUCTURE OF E. COLI KDO8P SYNTHASE
Components3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE
KeywordsLYASE / KDO / KDO8P / TIM BARREL / DAH7P / PEP / A5P
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 / Resolution: 2.4 Å
AuthorsRadaev, S. / Dastidar, P. / Patel, M. / Woodard, R.W. / Gatti, D.L.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Structure and mechanism of 3-deoxy-D-manno-octulosonate 8-phosphate synthase.
Authors: Radaev, S. / Dastidar, P. / Patel, M. / Woodard, R.W. / Gatti, D.L.
History
DepositionOct 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 11, 2017Group: Refinement description / Category: refine / Item: _refine.ls_percent_reflns_obs
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE
B: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE
C: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE
D: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,44314
Polymers123,4834
Non-polymers96110
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15330 Å2
ΔGint-203 kcal/mol
Surface area36820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.620, 228.620, 228.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein
3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE


Mass: 30870.676 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A715, EC: 4.1.2.16
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: AMMONIUM SULFATE, POTASSIUM PHOSPHATE, ETHYLENE GLYCOL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 23 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1400 mMpotassium phosphate1drop
21.4 Mammonium sulfate1drop
36 %ethylene glycol1drop
44 mMPEP1drop
54 mMarabimose 5-phosphate1drop
630 mg/mlprotein1drop
7400 mMpotassium phosphate1reservoir
86 %ethylene glycol1reservoir
91.7-1.9 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→22.86 Å / Num. obs: 76652 / % possible obs: 99.3 % / Redundancy: 20.6 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 22.3
Reflection shellResolution: 2.4→2.55 Å / Rmerge(I) obs: 0.564 / % possible all: 94.6
Reflection
*PLUS
Num. measured all: 1582716
Reflection shell
*PLUS
% possible obs: 94.6 % / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
SCALEPACKdata scaling
RefinementResolution: 2.4→22.86 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.239 7733 RANDOM
Rwork0.199 --
obs0.199 76652 -
Refinement stepCycle: LAST / Resolution: 2.4→22.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8144 0 50 446 8640
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.574
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_improper_angle_deg / Dev ideal: 1.012

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