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- PDB-1g7u: CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEX WITH S... -

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Basic information

Entry
Database: PDB / ID: 1g7u
TitleCRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEX WITH SUBSTRATE PHOSPHOENOL PYRUVATE
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
PHOSPHOENOLPYRUVATE / 2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 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, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues / 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

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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)31,0812
Polymers30,9131
Non-polymers1681
Water27015
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)124,3238
Polymers123,6514
Non-polymers6724
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 area16750 Å2
ΔGint-106 kcal/mol
Surface area38040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)117.900, 117.900, 117.900
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: 30912.754 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-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: MES 61mM pH 6.1, Glycerol 25% v/v, PEG 400 10% v/v, 3mg/mL PEP, 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
810 mMphosphoenolpyruvate1reservoir

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Dec 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 18541 / Num. obs: 7645 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Biso Wilson estimate: 51.113 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 6.9
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.066 / Num. unique all: 692 / % possible all: 85.3
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 85.8 %
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 85.3 % / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→8 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.281 317 random
Rwork0.228 --
obs0.231 6811 -
all-7985 -
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 10 15 2192
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_dihedral_angle_d26.1
X-RAY DIFFRACTIONx_improper_angle_d2.3
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 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_deg2.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.3

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