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Basic information

Entry
Database: PDB / ID: 2nxi
TitleStructural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase.
Components2-dehydro-3-deoxyphosphooctonate aldolase
KeywordsTRANSFERASE / KDO / KDO8P / KDO8PS / PEP / A5P
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
PHOSPHOENOLPYRUVATE / PHOSPHATE ION / 2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKona, F. / Xu, X. / Martin, P. / Kuzmic, P. / Gatti, D.L.
CitationJournal: Biochemistry / Year: 2007
Title: Structural and mechanistic changes along an engineered path from metallo to nonmetallo 3-deoxy-D-manno-octulosonate 8-phosphate synthases
Authors: Kona, F. / Xu, X. / Martin, P. / Kuzmic, P. / Gatti, D.L.
History
DepositionNov 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: 2-dehydro-3-deoxyphosphooctonate aldolase
D: 2-dehydro-3-deoxyphosphooctonate aldolase
E: 2-dehydro-3-deoxyphosphooctonate aldolase
F: 2-dehydro-3-deoxyphosphooctonate aldolase
G: 2-dehydro-3-deoxyphosphooctonate aldolase
H: 2-dehydro-3-deoxyphosphooctonate aldolase
I: 2-dehydro-3-deoxyphosphooctonate aldolase
J: 2-dehydro-3-deoxyphosphooctonate aldolase
K: 2-dehydro-3-deoxyphosphooctonate aldolase
L: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,87536
Polymers352,35412
Non-polymers3,52224
Water21,2221178
1
A: 2-dehydro-3-deoxyphosphooctonate aldolase
B: 2-dehydro-3-deoxyphosphooctonate aldolase
C: 2-dehydro-3-deoxyphosphooctonate aldolase
D: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,65012
Polymers117,4514
Non-polymers1,1988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16180 Å2
ΔGint-82 kcal/mol
Surface area33150 Å2
MethodPISA
2
E: 2-dehydro-3-deoxyphosphooctonate aldolase
F: 2-dehydro-3-deoxyphosphooctonate aldolase
G: 2-dehydro-3-deoxyphosphooctonate aldolase
H: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,65012
Polymers117,4514
Non-polymers1,1988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15920 Å2
ΔGint-84 kcal/mol
Surface area33520 Å2
MethodPISA
3
I: 2-dehydro-3-deoxyphosphooctonate aldolase
J: 2-dehydro-3-deoxyphosphooctonate aldolase
K: 2-dehydro-3-deoxyphosphooctonate aldolase
L: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,57612
Polymers117,4514
Non-polymers1,1258
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15900 Å2
ΔGint-86 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.883, 197.465, 124.874
Angle α, β, γ (deg.)90.00, 93.84, 90.00
Int Tables number4
Space group name H-MP1211

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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: 29362.830 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: kdsA / Production host: Escherichia coli (E. coli)
References: UniProt: O66496, 3-deoxy-8-phosphooctulonate synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H5O6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1178 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.56 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 161988 / Num. obs: 123597 / % possible obs: 76.3 % / Observed criterion σ(F): 4.4 / Observed criterion σ(I): 2.1 / Redundancy: 3.3 % / Biso Wilson estimate: 3.6 Å2 / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 8.3

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1FWN

1fwn


Resolution: 2.3→25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 653648.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.267 6233 5 %RANDOM
Rwork0.207 ---
obs0.207 123597 76.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.4769 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 55.2 Å2
Baniso -1Baniso -2Baniso -3
1--21.08 Å20 Å2-8.65 Å2
2--13.15 Å20 Å2
3---7.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24378 0 205 1178 25761
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.852.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 344 4.8 %
Rwork0.3 6898 -
obs--26.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4pep_a5p_mod5.parapep_a5p.toph

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