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- PDB-1gg0: CRYSTAL STRUCTURE ANALYSIS OF KDOP SYNTHASE AT 3.0 A -

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Basic information

Entry
Database: PDB / ID: 1gg0
TitleCRYSTAL STRUCTURE ANALYSIS OF KDOP SYNTHASE AT 3.0 A
Components3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE
KeywordsLYASE / beta-alpha-barrel
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
PHOSPHATE ION / 2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsWagner, T. / Kretsinger, R.H. / Bauerle, R. / Tolbert, W.D.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: 3-Deoxy-D-manno-octulosonate-8-phosphate synthase from Escherichia coli. Model of binding of phosphoenolpyruvate and D-arabinose-5-phosphate.
Authors: Wagner, T. / Kretsinger, R.H. / Bauerle, R. / Tolbert, W.D.
#1: Journal: 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.
#2: Journal: Proteins / Year: 1996
Title: Crystallization and preliminary crystallographic studies of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Escherichia coli
Authors: Tolbert, W.D. / Moll, J.R. / Bauerle, R. / Kretsinger, R.H.
History
DepositionAug 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0613
Polymers30,8711
Non-polymers1902
Water0
1
A: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE
hetero molecules

A: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE
hetero molecules

A: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE
hetero molecules

A: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,24212
Polymers123,4834
Non-polymers7608
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
MethodPQS
2
A: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE
hetero molecules

A: 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1216
Polymers61,7412
Non-polymers3804
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3810 Å2
ΔGint-40 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.167, 118.167, 118.167
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
DetailsThe biological assembly is a tetramer constructed from chain A and the symmetry partners generated by two two-fold axes.

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Components

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


Mass: 30870.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PCAM5 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A715, EC: 4.1.2.16
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 1500, 3-(N-morpholino)propanesulfonic acid, dithioerythitol, d-arabinose-5-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal grow
*PLUS
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220-28 %(w/wPEG15001reservoir
310 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: CUSTOM-MADE / Detector: AREA DETECTOR / Date: Mar 13, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 4988 / % possible obs: 88.6 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 43.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 9.8 / Num. unique all: 357 / % possible all: 62.9
Reflection
*PLUS
Num. measured all: 39075
Reflection shell
*PLUS
% possible obs: 62.9 %

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 3→20 Å / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.265 522 random
Rwork0.227 --
all0.231 4988 -
obs0.231 4988 -
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 10 0 2028
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg2.1
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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