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- PDB-3n9s: Class II fructose-1,6-bisphosphate aldolase from helicobacter pyl... -

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Basic information

Entry
Database: PDB / ID: 3n9s
TitleClass II fructose-1,6-bisphosphate aldolase from helicobacter pylori in complex with N-(4-hydroxybutyl)- glycolohydroxamic acid bis-phosphate, a competitive inhibitor
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE/LYASE INHIBITOR / FBP aldolase / Class II / inhibitor / LYASE / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


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
Chem-TD4 / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCoincon, M. / Sygusch, S.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Rational Design, Synthesis, and Evaluation of New Selective Inhibitors of Microbial Class II (Zinc Dependent) Fructose Bis-phosphate Aldolases.
Authors: Daher, R. / Fonvielle, M. / Gest, P.M. / Guerin, M.E. / Jackson, M. / Sygusch, J. / Therisod, M.
History
DepositionMay 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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

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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)68,50510
Polymers67,6022
Non-polymers9038
Water17,835990
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-72 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.959, 83.436, 139.985
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsdimeric

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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) / Strain: 51 / Gene: ALF_HELPY / Plasmid: pKK233-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: D0IR47, fructose-bisphosphate aldolase

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Non-polymers , 5 types, 998 molecules

#2: Chemical ChemComp-TD4 / 4-{hydroxy[(phosphonooxy)acetyl]amino}butyl dihydrogen phosphate


Mass: 323.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15NO10P2
#3: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 990 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 8.5
Details: 12% PEG 1000, 12% PEG 8000, 0.2 M Calcium Acetate,50 mM Tris/HOAc, pH 8.5, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.85→71.671 Å / Num. all: 50710 / Num. obs: 50710 / % possible obs: 98.1 % / Redundancy: 7.4 % / Rsym value: 0.161 / Net I/σ(I): 8.9
Reflection shell

Rmerge(I) obs: 0.013

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.957.50.65398472101.28497
1.95-2.077.515113868480.71597.4
2.07-2.217.51.54852365110.45597.7
2.21-2.397.42.24503060530.30798
2.39-2.627.42.94155456140.22598.4
2.62-2.937.44.23771451200.15598.6
2.93-3.387.35.63343145810.11198.9
3.38-4.147.27.32805538990.08499.2
4.14-5.8578.32162730750.0799.4
5.85-47.886.810.41223317990.05699.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHENIXdev_378refinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB enry 3c52

3c52


Resolution: 1.85→32.28 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.21 / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 3553 7.48 %
Rwork0.165 --
obs0.169 47476 91.63 %
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.278 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso max: 114.4 Å2 / Biso mean: 29.52 Å2 / Biso min: 8.55 Å2
Baniso -1Baniso -2Baniso -3
1--7.281 Å20 Å2-0 Å2
2--9.644 Å2-0 Å2
3----2.363 Å2
Refinement stepCycle: LAST / Resolution: 1.85→32.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 44 990 5686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064769
X-RAY DIFFRACTIONf_angle_d0.966413
X-RAY DIFFRACTIONf_chiral_restr0.057710
X-RAY DIFFRACTIONf_plane_restr0.005831
X-RAY DIFFRACTIONf_dihedral_angle_d15.8361799
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8750.2751200.2481429154975
1.875-1.9020.2831070.2371427153476
1.902-1.9310.2931260.2331471159779
1.931-1.9610.2771310.2241602173383
1.961-1.9930.281270.2141615174286
1.993-2.0270.2551320.2071695182789
2.027-2.0640.2711390.2011707184691
2.064-2.1040.241380.1991734187292
2.104-2.1470.2391460.1921781192793
2.147-2.1930.2371410.1811777191893
2.193-2.2440.2441420.1691752189493
2.244-2.30.2651430.1651766190993
2.3-2.3630.2241410.161766190793
2.363-2.4320.2171450.1571810195593
2.432-2.5110.2251460.161767191393
2.511-2.60.2291430.171796193994
2.6-2.7040.2131480.1591804195294
2.704-2.8270.2421480.1551817196595
2.827-2.9760.1881460.1591826197295
2.976-3.1630.2061510.1561851200296
3.163-3.4070.2061550.1471894204998
3.407-3.7490.1681560.1351904206098
3.749-4.290.1761550.1241926208198
4.29-5.4010.1781590.1361949210898
5.401-32.2850.1971680.1992057222598

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