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

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Basic information

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 / 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
PHOSPHOGLYCOLOHYDROXAMIC ACID / 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. / 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.
History
DepositionJan 12, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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_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_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_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_conn.ptnr2_symmetry / _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

Downloads & links

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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
Polymers78,1202
Non-polymers88112
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-321 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
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-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.5922, 0.8058, -0.007754), (0.8057, -0.5922, -0.0103), (-0.01289, -0.000147, -0.9999)
Vector: -36.93, 75.97, 241.5)

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 39059.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 CS520 / 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 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


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


Mass: 18.015 Da / Num. of mol.: 225 / 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: 4

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Sample preparation

CrystalDensity Matthews: 4.27 Å3/Da / Density % sol: 71 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.6 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlenzyme11
250 mMTris-HCl11
310 mMPGH11

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.033
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 248236 / % possible obs: 78.5 % / Redundancy: 5 % / Biso Wilson estimate: 24.01 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 1 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 1.4 / % possible all: 31.4
Reflection
*PLUS
Num. measured all: 55441
Reflection shell
*PLUS
% possible obs: 31.4 % / Mean I/σ(I) obs: 1.3

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZEN

1zen


Resolution: 2→30 Å / SU B: 4.1394 / SU ML: 0.10901 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17929 / ESU R Free: 0.16445
Details: INITIAL RIGID-BODY REFINEMENT USING RESTRAIN (DRIESSEN ET AL. (1989), J. APPL. CRYST. 22, PG 510-516).
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2768 5 %RANDOM
Rwork0.1916 ---
obs-55441 78.5 %-
Displacement parametersBiso mean: 26.59 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5248 0 30 225 5503
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.32
X-RAY DIFFRACTIONp_mcangle_it3.2993
X-RAY DIFFRACTIONp_scbond_it3.1822
X-RAY DIFFRACTIONp_scangle_it4.5283
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1770.15
X-RAY DIFFRACTIONp_singtor_nbd0.1820.3
X-RAY DIFFRACTIONp_multtor_nbd0.2740.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1890.3
X-RAY DIFFRACTIONp_planar_tor5.67
X-RAY DIFFRACTIONp_staggered_tor17.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS

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