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- PDB-1phw: Crystal structure of KDO8P synthase in its binary complex with su... -

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Basic information

Entry
Database: PDB / ID: 1phw
TitleCrystal structure of KDO8P synthase in its binary complex with substrate analog 1-deoxy-A5P
Components2-dehydro-3-deoxyphosphooctonate aldolase
KeywordsTRANSFERASE / BETA-ALPHA-BARRELS / LYASE / LIPOPOLYSACCHARIDE / A5P ANALOG
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
ANY 5'-MONOPHOSPHATE NUCLEOTIDE / 2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsVainer, R. / Belakhov, V. / Rabkin, E. / Baasov, T. / Adir, N.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structures of Escherichia coli KDO8P synthase complexes reveal the source of catalytic irreversibility.
Authors: Vainer, R. / Belakhov, V. / Rabkin, E. / Baasov, T. / Adir, N.
History
DepositionMay 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0852
Polymers30,8711
Non-polymers2141
Water61334
1
A: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules

A: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules

A: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules

A: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,3398
Polymers123,4834
Non-polymers8564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area15030 Å2
ΔGint-90 kcal/mol
Surface area38480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)118.258, 118.258, 118.258
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. The biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: x,y,z; -x,-y,z; -x,y,-z; x,y,-z;

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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


Mass: 30870.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: KDSA / Production host: Escherichia coli (E. coli)
References: UniProt: P0A715, 3-deoxy-8-phosphooctulonate synthase
#2: Chemical ChemComp-N / ANY 5'-MONOPHOSPHATE NUCLEOTIDE / 1-DEOXY-RIBOFURANOSE-5'-PHOSPHATE


Type: RNA linking / Mass: 214.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 6000, Glycrol, Tris-HCl , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 19, 2002 / Details: Bent mirror
RadiationMonochromator: Triangular mono chromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.36→45 Å / Num. all: 11488 / Num. obs: 11064 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.047 / Rsym value: 0.044 / Net I/σ(I): 17.6
Reflection shellResolution: 2.36→2.44 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1109 / Rsym value: 0.444 / % possible all: 97.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D9E (a)

1d9e


Resolution: 2.36→45 Å / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3127 925 -RANDOM
Rwork0.2366 ---
all0.3329 11488 --
obs0.2604 8958 78 %-
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.38 Å
Luzzati sigma a0.048 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 2.36→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 13 34 2129
LS refinement shellResolution: 2.36→2.41 Å
RfactorNum. reflection
Rfree0.3476 24
Rwork0.2859 -
obs-288

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