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- PDB-2yce: Structure of an Archaeal fructose-1,6-bisphosphate aldolase with ... -

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Basic information

Entry
Database: PDB / ID: 2yce
TitleStructure of an Archaeal fructose-1,6-bisphosphate aldolase with the catalytic Lys covalently bound to the carbinolamine intermediate of the substrate.
ComponentsFRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
KeywordsLYASE / GLYCOLYSIS
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / cytoplasm
Similarity search - Function
Aldolase FbaB-like, archaeal-type / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
D-MANNITOL-1,6-DIPHOSPHATE / Fructose-bisphosphate aldolase class 1
Similarity search - Component
Biological speciesTHERMOPROTEUS TENAX (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLorentzen, E. / Siebers, B. / Hensel, R. / Pohl, E.
CitationJournal: Biochemistry / Year: 2005
Title: Mechanism of the Schiff Base Forming Fructose-1,6-Bisphosphate Aldolase: Structural Analysis of Reaction Intermediates.
Authors: Lorentzen, E. / Siebers, B. / Hensel, R. / Pohl, E.
History
DepositionMar 14, 2011Deposition site: PDBE / Processing site: PDBE
SupersessionApr 27, 2011ID: 1W8R
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
B: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
C: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
D: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
E: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
F: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
G: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
H: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
I: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
J: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,83220
Polymers287,41110
Non-polymers3,42110
Water27,3471518
1
A: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
B: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
C: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
D: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
E: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,41610
Polymers143,7055
Non-polymers1,7115
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18030 Å2
ΔGint-59.1 kcal/mol
Surface area40360 Å2
MethodPISA
2
F: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
G: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
H: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
I: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
J: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,41610
Polymers143,7055
Non-polymers1,7115
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18060 Å2
ΔGint-58.2 kcal/mol
Surface area39880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.900, 159.200, 101.400
Angle α, β, γ (deg.)90.00, 107.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS 1 / FRUCTOSE-BIPHOSPHATE ALDOLASE CLASS I / FBP ALDOLASE


Mass: 28741.064 Da / Num. of mol.: 10 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: K177 COVALENTLY LINKED TO THE CARBINOLAMINE FORM OF THE SUBSTRATE FBP
Source: (gene. exp.) THERMOPROTEUS TENAX (unknown) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P58315, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-M2P / D-MANNITOL-1,6-DIPHOSPHATE / 1,6-DI-O-PHOSPHONO-D-MANNITOL


Mass: 342.132 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H16O12P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1518 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN A, ALA 173 TO SER ...ENGINEERED RESIDUE IN CHAIN A, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN A, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN B, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN B, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN C, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN C, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN D, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN D, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN E, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN E, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN F, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN F, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN G, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN G, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN H, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN H, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN I, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN I, ALA 173 TO SER ENGINEERED RESIDUE IN CHAIN J, TYR 146 TO PHE ENGINEERED RESIDUE IN CHAIN J, ALA 173 TO SER
Nonpolymer detailsM2P: THE SUBSTRATE FRUCTOSE 1,6-BISPHOSPHATE IS COVALENTLY LINKED TO THE CATALYTIC LYSINE AS A ...M2P: THE SUBSTRATE FRUCTOSE 1,6-BISPHOSPHATE IS COVALENTLY LINKED TO THE CATALYTIC LYSINE AS A CARBINOLAMINE FORM.

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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 Å3/Da / Density % sol: 40 % / Description: SOLVED BY RIGID BODY REFINEMENT OF 1OJX.
Crystal growpH: 5
Details: 9% (W/V) PEG 4000, 0.1 M NAACETATE PH 5.0, 1-8% GLYCEROL, 100 MM FBP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.812
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 1.93→40 Å / Num. obs: 179009 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.2
Reflection shellResolution: 1.93→2.02 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.2 / % possible all: 77.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OJX
Resolution: 1.93→39.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.061 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.19811 2723 1.5 %RANDOM
Rwork0.15592 ---
obs0.15654 179009 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.06 Å2
2--0.06 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.93→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19381 0 200 1518 21099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02220162
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9827292
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72252522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89223.161851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.504153382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.85515151
X-RAY DIFFRACTIONr_chiral_restr0.1090.23017
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115111
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6571.512444
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.125219925
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.15837708
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3954.57354
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.931→1.981 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 148 -
Rwork0.223 9800 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.1916-0.2965-0.13510.84820.02581.6116-0.00270.04520.2759-0.02620.0111-0.1402-0.24240.101-0.00840.0547-0.0284-0.00820.01770.01120.0956-2.6703126.281917.3401
21.07130.1988-0.13261.1141-0.01171.07420.0246-0.22840.09170.1219-0.0188-0.0487-0.06440.0867-0.00580.0304-0.0003-0.02010.0733-0.03320.0341-5.3635116.90850.2377
31.65490.32380.05871.21520.6171.39820.011-0.3197-0.32110.2256-0.0284-0.08910.29350.02630.01740.10770.01390.00050.09260.08990.0918-12.382483.370251.1022
41.34880.09670.11571.0372-0.2111.7099-0.01130.0567-0.3585-0.04490.0104-0.04930.27570.05360.0010.07820.00380.02420.005-0.02220.159-14.301571.981318.8387
51.2293-0.16640.10851.51960.12410.78650.02130.2972-0.0253-0.2231-0.0215-0.0728-0.02310.0820.00020.0399-0.01050.01480.1068-0.02130.0137-8.246598.3651-2.2534
61.3260.05440.01391.01070.37871.5317-0.02220.11960.3662-0.10570.00240.0287-0.324-0.10560.01980.10190.0303-0.02320.03550.03840.1565-43.0245134.178615.2551
71.26450.1467-0.15671.0620.00771.34310.0436-0.22290.27120.0644-0.04860.0876-0.1651-0.06880.00490.04070.02010.00270.095-0.08950.0987-45.0514126.362548.525
81.41870.29720.44561.33680.09510.94110.0659-0.3559-0.08210.185-0.06260.05020.0675-0.1949-0.00330.0508-0.03510.0190.14410.01640.0171-52.049192.961951.3163
91.361-0.21470.16080.8055-0.17641.57140.03240.0285-0.2659-0.04590.02980.10770.2273-0.1132-0.06230.0562-0.0364-0.00220.0272-0.01150.0753-54.368780.013419.6841
100.9807-0.1611-0.12021.3213-0.23841.03620.00840.2102-0.0112-0.1757-0.02810.06860.0428-0.11490.01970.0303-0.004-0.00810.10370.01370.0201-48.7818105.4234-2.5236
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 252
2X-RAY DIFFRACTION2B2 - 253
3X-RAY DIFFRACTION3C3 - 252
4X-RAY DIFFRACTION4D3 - 252
5X-RAY DIFFRACTION5E3 - 257
6X-RAY DIFFRACTION6F3 - 252
7X-RAY DIFFRACTION7G3 - 252
8X-RAY DIFFRACTION8H3 - 252
9X-RAY DIFFRACTION9I3 - 252
10X-RAY DIFFRACTION10J3 - 252

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