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- PDB-1fx6: AQUIFEX AEOLICUS KDO8P SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1fx6
TitleAQUIFEX AEOLICUS KDO8P SYNTHASE
Components2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
KeywordsLYASE / kdo8ps / kdo8p / kdo / PEP / A5P / beta/alpha barrel
Function / homology
Function and homology information


monosaccharide biosynthetic process / 3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / 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 speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.06 Å
AuthorsDuewel, H.S. / Radaev, S. / Wang, J. / Woodard, R.W. / Gatti, D.L.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Substrate and metal complexes of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Aquifex aeolicus at 1.9-A resolution. Implications for the condensation mechanism.
Authors: Duewel, H.S. / Radaev, S. / Wang, J. / Woodard, R.W. / Gatti, D.L.
History
DepositionSep 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Feb 7, 2024Group: 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: 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
B: 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7394
Polymers59,5492
Non-polymers1902
Water4,576254
1
A: 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
B: 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
hetero molecules

A: 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
B: 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,4788
Polymers119,0984
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area13450 Å2
ΔGint-86 kcal/mol
Surface area35070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.589, 84.589, 159.634
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
DetailsThe biological assembly is a tetramer constructed from chain A and chain B and their symmetry partners generated by application of the symmetry operation (x=y, y=x, z=-z)

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Components

#1: Protein 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE / E.C.4.1.2.16 / KDO8P SYNTHASE / PHOSPHO-2-DEHYDRO-3-DEOXYOCTONATE ALDOLASE / 3-DEOXY-D-MANNO-OCTULOSONIC ACID 8- ...KDO8P SYNTHASE / PHOSPHO-2-DEHYDRO-3-DEOXYOCTONATE ALDOLASE / 3-DEOXY-D-MANNO-OCTULOSONIC ACID 8-PHOSPHATE SYNTHETASE / KDO-8-PHOSPHATE SYNTHETASE


Mass: 29774.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: PAAKDSA / Production host: Escherichia coli (E. coli) / References: UniProt: O66496, EC: 4.1.2.16
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 100 mM Na-acetate, 6% PEG 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP at 278K, temperature 278.0K
Crystal grow
*PLUS
Temperature: 4 ℃
Details: drop contains protein and reservoir solution in a 1:1 ratio
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlenzyme1drop
2100 mMsodium acetate1reservoir
35-6 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→43.05 Å / Num. all: 34118 / Num. obs: 34118 / % possible obs: 81.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 17.5
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.461 / Num. unique all: 1641 / % possible all: 21.9
Reflection
*PLUS
Num. measured all: 362497
Reflection shell
*PLUS
% possible obs: 21.9 %

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Processing

Software
NameVersionClassification
CNS1refinement
FRAMBOdata collection
SIEMENSdata reduction
SAINTdata scaling
RefinementResolution: 2.06→43.05 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 8231969.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 3396 10 %RANDOM
Rwork0.216 ---
all-34118 --
obs-34118 81.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.38 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.32 Å26.47 Å20 Å2
2--7.32 Å20 Å2
3----14.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.06→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3963 0 10 254 4227
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 159 9.7 %
Rwork0.363 1482 -
obs--21.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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