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- PDB-3c52: Class II fructose-1,6-bisphosphate aldolase from helicobacter pyl... -

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Basic information

Entry
Database: PDB / ID: 3c52
TitleClass II fructose-1,6-bisphosphate aldolase from helicobacter pylori in complex with phosphoglycolohydroxamic acid, a competitive inhibitor
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / CLASS II / FBP / aldolase / glycolysis / inhibitor / Phosphoglycolohydroxamic acid / Metal-binding
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 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
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsCoincon, M. / Sygusch, J.
CitationJournal: Chemistry / Year: 2008
Title: Synthesis and Biochemical Evaluation of Selective Inhibitors of Class II Fructose Bisphosphate Aldolases: Towards New Synthetic Antibiotics.
Authors: Fonvielle, M. / Coincon, M. / Daher, R. / Desbenoit, N. / Kosieradzka, K. / Barilone, N. / Gicquel, B. / Sygusch, J. / Jackson, M. / Therisod, M.
History
DepositionJan 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 25, 2012Group: Structure summary
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase
B: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,20110
Polymers67,6022
Non-polymers5998
Water11,367631
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.242, 85.305, 90.818
Angle α, β, γ (deg.)90.00, 100.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fructose-bisphosphate aldolase /


Mass: 33800.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: fba / Plasmid: PKK233-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P56109, fructose-bisphosphate aldolase

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Non-polymers , 5 types, 639 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#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.: 631 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12% PEG 1000, 12% PEG 8000, 0.2 M Calcium Acetate,50 mM Tris/HOAc, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. all: 52225 / Num. obs: 37646 / % possible obs: 72.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.072 / Net I/σ(I): 12.75
Reflection shellResolution: 1.83→1.9 Å / % possible all: 0.176

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXAutoMRphasing
andrefinement
RefinementStarting model: free enzyme

Resolution: 2.3→32 Å / σ(F): 0.5 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: The Fridel pairs were used for phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2397 9.1 %RANDOM
Rwork0.204 ---
all-26250 --
obs-24022 91.5 %-
Solvent computationBsol: 40.127 Å2
Displacement parametersBiso mean: 34.759 Å2
Baniso -1Baniso -2Baniso -3
1--12.843 Å20 Å22.535 Å2
2--27.146 Å20 Å2
3----14.303 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3499 Å0.2843 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.284 Å
Refinement stepCycle: LAST / Resolution: 2.3→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4567 0 26 631 5224
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.134
X-RAY DIFFRACTIONf_mcbond_it1.2451.5
X-RAY DIFFRACTIONf_scbond_it4.5045.5
X-RAY DIFFRACTIONf_mcangle_it1.992
X-RAY DIFFRACTIONf_scangle_it5.4646.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5pgh.parpgh.top

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