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- PDB-1x6u: KDO8P synthase in it's binary complex with the product KDO8P -

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Basic information

Entry
Database: PDB / ID: 1x6u
TitleKDO8P synthase in it's binary complex with the product KDO8P
Components2-dehydro-3-deoxyphosphooctonate aldolase
KeywordsTRANSFERASE / KDO8P
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
Chem-DO8 / 2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionAug 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)31,1892
Polymers30,8711
Non-polymers3181
Water45025
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)124,7558
Polymers123,4834
Non-polymers1,2734
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 area16030 Å2
ΔGint-123 kcal/mol
Surface area38160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)118.530, 118.530, 118.530
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 generated from the dimer in the asymmetric unit by the operations: X,Y,Z -X,-Y,Z -X,Y,-Z X,-Y,-Z Z,X,Y Z,-X,-Y -Z,-X,Y -Z,X,-Y Y,Z,X -Y,Z,-X Y,-Z,-X -Y,-Z,X 1/2+X,1/2+Y,1/2+Z 1/2-X,1/2-Y,1/2+Z 1/2-X,1/2+Y,1/2-Z 1/2+X,1/2-Y,1/2-Z 1/2+Z,1/2+X,1/2+Y 1/2+Z,1/2-X,1/2-Y 1/2-Z,1/2-X,1/2+Y 1/2-Z,1/2+X,1/2-Y 1/2+Y,1/2+Z,1/2+X 1/2-Y,1/2+Z,1/2-X 1/2+Y,1/2-Z,1/2-X 1/2-Y,1/2-Z,1/2+X

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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: 30870.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kdsA / Plasmid: pJU1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: P0A715, 3-deoxy-8-phosphooctulonate synthase
#2: Sugar ChemComp-DO8 / 3-deoxy-8-O-phosphono-alpha-D-manno-oct-2-ulopyranosonic acid / 3-DEOXY-D-MANNO-2-OCTULOSONATE-8-PHOSPHATE / 3-deoxy-8-O-phosphono-alpha-D-manno-oct-2-ulosonic acid / 3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid / 3-deoxy-8-O-phosphono-manno-oct-2-ulosonic acid


Type: D-saccharide, alpha linking / Mass: 318.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15O11P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.2 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG4000, Glycerol, Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 6950 / % possible obs: 90.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Rsym value: 0.075 / Net I/σ(I): 13.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 5.3 / Num. unique all: 768 / % possible all: 99.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PHW

1phw


Resolution: 2.7→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 707 -RANDOM
Rwork0.239 ---
all0.239 6950 --
obs0.239 5829 75.3 %-
Displacement parametersBiso mean: 66.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 20 25 2126
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.68
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1.19

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