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- PDB-1b57: CLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE IN COMPLEX WITH PHOSP... -

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Entry
Database: PDB / ID: 1b57
TitleCLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE IN COMPLEX WITH PHOSPHOGLYCOLOHYDROXAMATE
ComponentsPROTEIN (FRUCTOSE-BISPHOSPHATE ALDOLASE II)
KeywordsLYASE / ALDEHYDE / GLYCOLYSIS
Function / homologyFructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase, class II, yeast/E. coli subtype / Aldolase-type TIM barrel / Fructose-bisphosphate aldolase class-II / Fructose-bisphosphate aldolase class-II signature 1. / Fructose-bisphosphate aldolase class-II signature 2. / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / gluconeogenesis / glycolytic process ...Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase, class II, yeast/E. coli subtype / Aldolase-type TIM barrel / Fructose-bisphosphate aldolase class-II / Fructose-bisphosphate aldolase class-II signature 1. / Fructose-bisphosphate aldolase class-II signature 2. / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / gluconeogenesis / glycolytic process / zinc ion binding / identical protein binding / plasma membrane / cytosol / Fructose-bisphosphate aldolase class 2
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2 Å resolution
AuthorsHall, D.R. / Hunter, W.N.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: The crystal structure of Escherichia coli class II fructose-1, 6-bisphosphate aldolase in complex with phosphoglycolohydroxamate reveals details of mechanism and specificity.
Authors: Hall, D.R. / Leonard, G.A. / Reed, C.D. / Watt, C.I. / Berry, A. / Hunter, W.N.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Conserved Residues in the Mechanism of the E. Coli Class II Fbp-Aldolase
Authors: Plater, A.R. / Zgiby, S.M. / Thomson, G.J. / Qamar, S. / Wharton, C.W. / Berry, A.
#2: Journal: Structure / Year: 1996
Title: The Crystal Structure of a Class II Fructose-1,6-Bisphosphate Aldolase Shows a Novel Binuclear Metal-Binding Active Site Embedded in a Familiar Fold
Authors: Cooper, S.J. / Leonard, G.A. / Mcsweeney, S.M. / Thompson, A.W. / Naismith, J.H. / Qamar, S. / Plater, A. / Berry, A. / Hunter, W.N.
#3: Journal: Nat.Struct.Biol. / Year: 1996
Title: Novel Active Site in Escherichia Coli Fructose 1,6-Bisphosphate Aldolase
Authors: Blom, N.S. / Tetreault, S. / Coulombe, R. / Sygusch, J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 12, 1999 / Release: Jan 7, 2000
RevisionDateData content typeGroupProviderType
1.0Jan 7, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (FRUCTOSE-BISPHOSPHATE ALDOLASE II)
B: PROTEIN (FRUCTOSE-BISPHOSPHATE ALDOLASE II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,00114
Polyers78,1202
Non-polymers88112
Water4,053225
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)7220
ΔGint (kcal/M)-321
Surface area (Å2)24380
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)78.237, 78.237, 289.687
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP 31 2 1

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide PROTEIN (FRUCTOSE-BISPHOSPHATE ALDOLASE II) / E.C.4.1.2.13 LYASE


Mass: 39059.957 Da / Num. of mol.: 2 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Strain: K12 CS520 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P0AB71, fructose-bisphosphate aldolase

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Non-polymers , 5 types, 237 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Formula: Zn / Zinc
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Formula: Na / Sodium
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Formula: Cl / Chloride
#5: Chemical ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 2 / Formula: C2H6NO6P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 4.27 / Density percent sol: 71 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temp: 4 ℃ / pH: 7.6 / Method: batch method
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
120 mg/mlenzyme11
250 mMTris-HCl11
310 mMPGH11

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Data collection

DiffractionMean temperature: 287 kelvins
SourceSource: SYNCHROTRON / Type: ESRF BEAMLINE BM14 / Synchrotron site: ESRF / Beamline: BM14 / Wavelength: 1.033
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Apr 1, 1997
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 24.01 Å2 / D resolution high: 2 Å / D resolution low: 3 Å / Number obs: 248236 / Rmerge I obs: 0.07 / NetI over sigmaI: 16.7 / Redundancy: 5 % / Percent possible obs: 78.5
Reflection shellRmerge I obs: 0.224 / Highest resolution: 2 Å / Lowest resolution: 2.05 Å / MeanI over sigI obs: 1.4 / Redundancy: 1 % / Percent possible all: 31.4
Reflection
*PLUS
Number measured all: 55441
Reflection shell
*PLUS
Percent possible obs: 31.4 / MeanI over sigI obs: 1.3

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZEN
Details: INITIAL RIGID-BODY REFINEMENT USING RESTRAIN (DRIESSEN ET AL. (1989), J. APPL. CRYST. 22, PG 510-516).
Overall SU B: 4.1394 / Overall SU ML: 0.10901 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.17929 / Overall ESU R Free: 0.16445
Displacement parametersB iso mean: 26.59 Å2
Least-squares processR factor R free: 0.23 / R factor R work: 0.1916 / Highest resolution: 2 Å / Lowest resolution: 3 Å / Number reflection R free: 2768 / Number reflection obs: 55441 / Percent reflection R free: 5 / Percent reflection obs: 78.5
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 5248 / Nucleic acid: 0 / Ligand: 30 / Solvent: 225 / Total: 5503
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.020
X-RAY DIFFRACTIONp_angle_d0.0320.040
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.050
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.3002.000
X-RAY DIFFRACTIONp_mcangle_it3.2993.000
X-RAY DIFFRACTIONp_scbond_it3.1822.000
X-RAY DIFFRACTIONp_scangle_it4.5283.000
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1770.150
X-RAY DIFFRACTIONp_singtor_nbd0.1820.300
X-RAY DIFFRACTIONp_multtor_nbd0.2740.300
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1890.300
X-RAY DIFFRACTIONp_planar_tor5.67.0
X-RAY DIFFRACTIONp_staggered_tor17.315.0
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.320.0
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Least-squares process
*PLUS
R factor R work: 0.192

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