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- PDB-1gyn: Class II fructose 1,6-bisphosphate aldolase with Cadmium (not Zin... -

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Basic information

Entry
Database: PDB / ID: 1gyn
TitleClass II fructose 1,6-bisphosphate aldolase with Cadmium (not Zinc) in the active site
ComponentsFRUCTOSE-BISPHOSPHATE ALDOLASE II
KeywordsLYASE / CADMIUM / ALDOLASE
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / gluconeogenesis / glycolytic process / protein homodimerization activity / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase, class II, yeast/E. coli subtype / Fructose-bisphosphate aldolase class-II signature 1. / Fructose-bisphosphate aldolase class-II signature 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
: / Fructose-bisphosphate aldolase class 2 / Fructose-bisphosphate aldolase class 2
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHall, D.R. / Kemp, L.E. / Leonard, G.A. / Berry, A. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: The Organization of Divalent Cations in the Active Site of Cadmium Escherichia Coli Fructose 1,6-Bisphosphate Aldolase
Authors: Hall, D.R. / Kemp, L.E. / Leonard, G.A. / Marshall, K. / Berry, A. / Hunter, W.N.
History
DepositionApr 27, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY A 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRUCTOSE-BISPHOSPHATE ALDOLASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6226
Polymers39,0601
Non-polymers5625
Water2,900161
1
A: FRUCTOSE-BISPHOSPHATE ALDOLASE II
hetero molecules

A: FRUCTOSE-BISPHOSPHATE ALDOLASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,24412
Polymers78,1202
Non-polymers1,12410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_575x,x-y+2,-z+1/61
MethodPQS
Unit cell
Length a, b, c (Å)77.331, 77.331, 290.851
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein FRUCTOSE-BISPHOSPHATE ALDOLASE II / FBP ALDOLASE


Mass: 39059.957 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: P11604, UniProt: P0AB71*PLUS, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES THE CONVERSION OF FRUCTOSE 1,6-BISPHOSPHATE TO GLYCERONE PHOSPHATE AND D-GLYCERALDEHYDE 3- ...CATALYZES THE CONVERSION OF FRUCTOSE 1,6-BISPHOSPHATE TO GLYCERONE PHOSPHATE AND D-GLYCERALDEHYDE 3-PHOSPHATE. THE BIOLOGICAL UNIT OF THIS PROTEIN IS A HOMODIMER, AND BELONGS TO THE CALSS II FAMILY OF FRUCTOSE-BISPHOSPHATE ALDOLASE PROTEINS. THIS ENZYME FORMS PART OF THE GLYCOLYSIS PATHWAY.

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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: 3.22 Å3/Da / Density % sol: 61.5 %
Crystal growpH: 7.6 / Details: pH 7.60
Crystal grow
*PLUS
pH: 7.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
116.5 mg/mlenzyme11
250 mMTris-HCl11pH7.5
33-4 %(w/v)PEG400011
42 mM11CdCl2

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.033
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2→38.3 Å / Num. obs: 31355 / % possible obs: 86.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 1.3 / % possible all: 51
Reflection
*PLUS
Num. measured all: 102727 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 51 % / Rmerge(I) obs: 0.29

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZEN

1zen


Resolution: 2→38.35 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.635 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1580 5 %RANDOM
Rwork0.168 ---
obs0.169 29766 87.2 %-
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: 25.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 5 161 2704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212593
X-RAY DIFFRACTIONr_bond_other_d00.022299
X-RAY DIFFRACTIONr_angle_refined_deg2.561.943520
X-RAY DIFFRACTIONr_angle_other_deg1.24335371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4433330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97115432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1820.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022923
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02495
X-RAY DIFFRACTIONr_nbd_refined0.2530.3571
X-RAY DIFFRACTIONr_nbd_other0.2150.32223
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.3460.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.5167
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3250.53
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.327
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.517
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6061.51649
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.77122639
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3313944
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.8384.5881
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.349 42
Rwork0.25 1289
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 38.3 Å / Rfactor Rfree: 0.193 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.6
LS refinement shell
*PLUS
Rfactor Rfree: 0.35

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