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- PDB-1rvg: crystal structure of class II fructose-bisphosphate aldolase from... -

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Basic information

Entry
Database: PDB / ID: 1rvg
Titlecrystal structure of class II fructose-bisphosphate aldolase from Thermus aquaticus in complex with Y
Componentsfructose-1,6-bisphosphate aldolase
KeywordsLYASE / CLASS II ALDOLASE / METAL-DEPDENDENT ALDOLASE
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / glycolytic process / zinc ion binding
Similarity search - Function
Fructose-1,6-bisphosphate aldolase, class 2 / : / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / YTTRIUM (III) ION / Fructose-1,6-bisphosphate aldolase
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsIzard, T. / Sygusch, J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Induced Fit Movements and Metal Cofactor Selectivity of Class II Aldolases: STRUCTURE OF THERMUS AQUATICUS FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE.
Authors: Izard, T. / Sygusch, J.
History
DepositionDec 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 2, 2020Group: Advisory / Derived calculations / Structure summary
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct / struct_conn / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct.title / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: fructose-1,6-bisphosphate aldolase
B: fructose-1,6-bisphosphate aldolase
C: fructose-1,6-bisphosphate aldolase
D: fructose-1,6-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,10025
Polymers132,5684
Non-polymers1,53221
Water17,547974
1
A: fructose-1,6-bisphosphate aldolase
B: fructose-1,6-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,17214
Polymers66,2842
Non-polymers88812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-190 kcal/mol
Surface area23060 Å2
MethodPISA
2
C: fructose-1,6-bisphosphate aldolase
D: fructose-1,6-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,92811
Polymers66,2842
Non-polymers6449
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-144 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.860, 57.550, 138.617
Angle α, β, γ (deg.)90.00, 90.26, 90.00
Int Tables number3
Space group name H-MP121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
fructose-1,6-bisphosphate aldolase


Mass: 33141.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RHA2, fructose-bisphosphate aldolase

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Non-polymers , 5 types, 995 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Co
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Y
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 974 / 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: 3 Å3/Da / Density % sol: 59.05 %
Crystal grow
*PLUS
Temperature: 295 K / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.75 mg/mlprotein1drop
22 mMsucrose monolaurate1drop
31.7 Mammonium sulfate1reservoir
40.1 MTris-HCl1reservoirpH7.5
510 mM1reservoirCoCl2

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.105 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.105 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 99328 / % possible obs: 92.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 23.2 Å2
Reflection
*PLUS
Highest resolution: 2 Å / Redundancy: 9.2 % / Num. measured all: 912165 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 92.9 % / Rmerge(I) obs: 0.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→40 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1838787.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The authors used Sr scattering factors which are virtually identical to those of Yttrium for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 4949 5 %RANDOM
Rwork0.225 ---
all0.225 ---
obs0.225 98502 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.949 Å2 / ksol: 0.359181 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1-13.17 Å20 Å21.22 Å2
2---7.13 Å20 Å2
3----6.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9343 0 65 974 10382
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 794 4.9 %
Rwork0.358 15451 -
obs--91.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER-TOPOLOGY
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40.6 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Highest resolution: 2 Å

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