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- PDB-1g7v: CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEXES WITH... -

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Basic information

Entry
Database: PDB / ID: 1g7v
TitleCRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEXES WITH THE MECHANISM-BASED INHIBITOR
Components2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
KeywordsLYASE / beta-alpha-barrels / lipopolysaccharide
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-PAI / 2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAsojo, O.A. / Friedman, J.M. / Belakhov, V. / Shoham, Y. / Adir, N. / Baasov, T.
CitationJournal: Biochemistry / Year: 2001
Title: Crystal structures of KDOP synthase in its binary complexes with the substrate phosphoenolpyruvate and with a mechanism-based inhibitor.
Authors: Asojo, O. / Friedman, J. / Adir, N. / Belakhov, V. / Shoham, Y. / Baasov, T.
History
DepositionNov 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2862
Polymers30,8711
Non-polymers4151
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)125,1448
Polymers123,4834
Non-polymers1,6614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_576x,-y+2,-z+11
Buried area18000 Å2
ΔGint-85 kcal/mol
Surface area36760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)117.600, 117.600, 117.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE / 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) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A715, EC: 4.1.2.16
#2: Chemical ChemComp-PAI / {[(2,2-DIHYDROXY-ETHYL)-(2,3,4,5-TETRAHYDROXY-6-PHOSPHONOOXY-HEXYL)-AMINO]-METHYL}-PHOSPHONIC ACID


Mass: 415.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H23NO13P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: MES or MOPS 61mM pH 6.1, 25% v/v Glycerol, 20mg/mL protein in tris buffer, 30 microgram/mL inhibitor, 10% v/v PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-HCl1drop
20.02 %beta-mercaptoethanol1drop
30.02 %sodium azide1drop
445 mg/mlprotein1drop
561 mMMOPS1reservoir
625 %(v/v)glycerol1reservoir
710 %(v/v)PEG4001reservoir
80.053 mMinhibitor 21reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.98104, 0.98066, 0.97719
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: 1997
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981041
20.980661
30.977191
ReflectionResolution: 2.27→30 Å / Num. all: 30388 / Num. obs: 26690 / % possible obs: 71 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.143 / % possible all: 47.4
Reflection
*PLUS
Highest resolution: 2.23 Å / Lowest resolution: 20 Å / % possible obs: 70.6 %
Reflection shell
*PLUS
Highest resolution: 2.23 Å / Lowest resolution: 2.3 Å / % possible obs: 14.1 % / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→8 Å / σ(F): 3 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.242 360 Random
Rwork0.221 --
obs0.225 7041 -
all-7501 -
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 25 21 2210
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_improper_angle_d2.2
X-RAY DIFFRACTIONx_angle_deg2.4
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.2

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