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- PDB-3c4u: Structure of class II fructose-biphosphate aldolase from helicoba... -

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Basic information

Entry
Database: PDB / ID: 3c4u
TitleStructure of class II fructose-biphosphate aldolase from helicobacter pylori
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / FBP aldolase / Class II / ZINC / glycolysis / 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
Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.83 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 1.2Aug 30, 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 / 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 / _struct_ref_seq_dif.details / _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: Fructose-bisphosphate aldolase
B: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7786
Polymers67,6022
Non-polymers1774
Water16,808933
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.023, 82.560, 91.272
Angle α, β, γ (deg.)90.000, 99.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 933 / 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: 2.14 Å3/Da / Density % sol: 42.58 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. all: 72445 / Num. obs: 71999 / % possible obs: 99.4 % / Redundancy: 8.64 % / Biso Wilson estimate: 10.93 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.245 / Net I/σ(I): 18.5
Reflection shellResolution: 1.62→1.68 Å / Mean I/σ(I) obs: 6.4 / Num. unique all: 7031 / Rsym value: 0.697 / % possible all: 0.983

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
CNSrefinement
RefinementStarting model: PDB ENTRY 1RVG

1rvg


Resolution: 1.83→33.404 Å / FOM work R set: 0.824 / Cross valid method: THROUGHOUT / σ(I): 1 / Stereochemistry target values: ML / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.207 4824 10.07 %RANDOM
Rwork0.186 ---
obs0.188 47885 95.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.259 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 1.27 Å2 / Biso mean: 17.42 Å2 / Biso min: 70.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.725 Å20 Å20.263 Å2
2--3.679 Å2-0 Å2
3----1.954 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.197 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.197 Å
Refinement stepCycle: LAST / Resolution: 1.83→33.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4520 0 4 933 5457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044600
X-RAY DIFFRACTIONf_angle_d0.5736184
X-RAY DIFFRACTIONf_chiral_restr0.035688
X-RAY DIFFRACTIONf_plane_restr0.002806
X-RAY DIFFRACTIONf_dihedral_angle_d14.8711708
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.83-1.8510.2621380.231312145088
1.851-1.8730.2791410.2271325146689
1.873-1.8950.2621360.2221365150189
1.895-1.9190.2461710.231331150291
1.919-1.9450.251620.2131368153089
1.945-1.9710.2411480.2231349149791
1.971-20.2521590.2071368152792
2-2.0290.2151730.1971371154492
2.029-2.0610.261600.2061430159094
2.061-2.0950.221370.2051384152194
2.095-2.1310.2071440.1921450159495
2.131-2.170.2011770.1811470164796
2.17-2.2110.2211610.1961388154996
2.211-2.2570.2081630.1861449161295
2.257-2.3060.2131690.1841450161996
2.306-2.3590.2171770.1811420159796
2.359-2.4180.231680.1931459162796
2.418-2.4840.251730.1971425159896
2.484-2.5570.2121520.1891489164198
2.557-2.6390.2091660.1891471163797
2.639-2.7330.2061510.1891479163098
2.733-2.8430.2131790.1881464164397
2.843-2.9720.1831660.1781482164898
2.972-3.1290.1711720.1821464163698
3.129-3.3240.1761660.1641517168399
3.324-3.5810.1911660.1571509167599
3.581-3.9410.1581790.1561500167999
3.941-4.510.1581660.1471495166199
4.51-5.6770.1811630.1641546170999
5.677-33.410.2281410.191531167297

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