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- PDB-1o60: Crystal structure of KDO-8-phosphate synthase -

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Basic information

Entry
Database: PDB / ID: 1o60
TitleCrystal structure of KDO-8-phosphate synthase
Components2-dehydro-3-deoxyphosphooctonate aldolase
KeywordsTRANSFERASE / structural genomics
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 / cytoplasm
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 speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-Met SAD phasing / Resolution: 1.8 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionOct 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: 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 / Item: _software.name
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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)129,5874
Polymers129,5874
Non-polymers00
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12300 Å2
ΔGint-74 kcal/mol
Surface area36990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.965, 92.893, 82.301
Angle α, β, γ (deg.)90.00, 116.82, 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: 32396.643 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: KDSA, HI1557 / Production host: Escherichia coli (E. coli)
References: UniProt: P45251, 3-deoxy-8-phosphooctulonate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 293 K / Method: hanging drop vapor diffusion / pH: 7.5
Components of the solutions
IDConc.NameCrystal-IDSol-ID
117mg/ml protein11
2150mM NaCl12
310mM Hepes12
41mM beta-mercaptoethanol12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9796 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.8→39.22 Å / Num. all: 95693 / Num. obs: 95693 / % possible obs: 97.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 5.5 / % possible all: 97.7
Reflection shell
*PLUS
% possible obs: 97.7 %

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Processing

Software
NameVersionClassification
REFMAC4refinement
MOSFLMdata reduction
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: Se-Met SAD phasing / Resolution: 1.8→39.22 Å / σ(F): 0
RfactorNum. reflection
Rfree0.242 9540
Rwork0.207 -
obs-95689
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 247.859 Å2 / ksol: 0.968 e/Å3
Displacement parametersBiso mean: 24.423 Å2
Baniso -1Baniso -2Baniso -3
1--0.492 Å20 Å20.015 Å2
2--0.745 Å20 Å2
3----0.24 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 1.8→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8216 0 0 568 8784
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d2.045
X-RAY DIFFRACTIONp_planar_tor2.907
X-RAY DIFFRACTIONp_chiral_restr0.124
X-RAY DIFFRACTIONp_plane_restr0.012
X-RAY DIFFRACTIONp_mcbond_it1.572
X-RAY DIFFRACTIONp_mcangle_it2.773
X-RAY DIFFRACTIONp_scbond_it3.068
X-RAY DIFFRACTIONp_scangle_it4.541
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2

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