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- PDB-3n9r: Class II fructose-1,6-bisphosphate aldolase from helicobacter pyl... -

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Basic information

Entry
Database: PDB / ID: 3n9r
TitleClass II fructose-1,6-bisphosphate aldolase from helicobacter pylori in complex with N-(4-hydroxybutyl)-phosphoglycolohydroxamic acid, a competitive inhibitor
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / FBP aldolase / Class II / inhibitor
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-TD3 / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
K: Fructose-bisphosphate aldolase
P: Fructose-bisphosphate aldolase
U: Fructose-bisphosphate aldolase
Z: Fructose-bisphosphate aldolase
e: Fructose-bisphosphate aldolase
j: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,34340
Polymers270,4068
Non-polymers2,93632
Water50,1362783
1
A: Fructose-bisphosphate aldolase
e: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,33610
Polymers67,6022
Non-polymers7348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-73 kcal/mol
Surface area22590 Å2
MethodPISA
2
j: Fructose-bisphosphate aldolase
hetero molecules

B: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,33610
Polymers67,6022
Non-polymers7348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4090 Å2
ΔGint-59 kcal/mol
Surface area22590 Å2
MethodPISA
3
K: Fructose-bisphosphate aldolase
hetero molecules

Z: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,33610
Polymers67,6022
Non-polymers7348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4250 Å2
ΔGint-73 kcal/mol
Surface area22470 Å2
MethodPISA
4
P: Fructose-bisphosphate aldolase
hetero molecules

U: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,33610
Polymers67,6022
Non-polymers7348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area4280 Å2
ΔGint-73 kcal/mol
Surface area22550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.400, 104.400, 111.900
Angle α, β, γ (deg.)98.500, 90.000, 90.000
Int Tables number1
Space group name H-MP1
Detailsdimeric

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Components

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Protein , 1 types, 8 molecules ABKPUZej

#1: Protein
Fructose-bisphosphate aldolase /


Mass: 33800.812 Da / Num. of mol.: 8
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, 2815 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-TD3 / 2-[hydroxy(4-hydroxybutyl)amino]-2-oxoethyl dihydrogen phosphate


Mass: 243.152 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14NO7P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2783 / 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: 43.99 %
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 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.798→46.631 Å / Num. all: 205157 / Num. obs: 205157 / % possible obs: 96 % / Redundancy: 3 % / Rsym value: 0.087 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.930.32.388149296090.394.4
1.9-2.0130.2073.383309280500.20795.3
2.01-2.1530.1484.578725264890.14895.3
2.15-2.3230.1135.673757248410.11396.1
2.32-2.5530.099667667228570.09996.5
2.55-2.8530.0886.261429207940.08896.9
2.85-3.292.90.0796.654287184220.07997.4
3.29-4.022.90.0677.345516156470.06797.8
4.02-5.692.90.0617.635460120700.06197.7
5.69-46.6330.0637.21889863780.06394.6

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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: 3C52

3c52


Resolution: 1.8→41.529 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.19 / σ(F): 1.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 31924 8 %
Rwork0.158 --
obs0.162 398819 93.48 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.715 Å2 / ksol: 0.414 e/Å3
Displacement parametersBiso max: 137.96 Å2 / Biso mean: 28.685 Å2 / Biso min: 6.84 Å2
Baniso -1Baniso -2Baniso -3
1--2.123 Å2-0.151 Å2-0.299 Å2
2--3.533 Å2-1.178 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18336 0 144 2783 21263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00718768
X-RAY DIFFRACTIONf_angle_d0.98325216
X-RAY DIFFRACTIONf_chiral_restr0.0612800
X-RAY DIFFRACTIONf_plane_restr0.0063264
X-RAY DIFFRACTIONf_dihedral_angle_d14.3337048
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 (%)
1.8-1.8210.27410730.241122531332693
1.821-1.8420.27410590.232121861324593
1.842-1.8640.25910780.222123581343695
1.864-1.8880.25410550.205121411319693
1.888-1.9130.25110650.207122361330193
1.913-1.9390.24510880.199125041359295
1.939-1.9670.24410660.193121921325893
1.967-1.9960.23110630.187122231328694
1.996-2.0270.22310750.179123421341795
2.027-2.060.21810640.177122621332693
2.06-2.0960.21910720.17122421331495
2.096-2.1340.2210780.169124071348594
2.134-2.1750.21210580.156122601331894
2.175-2.220.20110700.155123501342094
2.22-2.2680.20610700.149123121338294
2.268-2.320.21310690.158122441331394
2.32-2.3790.20610630.152122381330194
2.379-2.4430.18810530.142122061325993
2.443-2.5150.21110680.151122831335194
2.515-2.5960.20410580.151122391329793
2.596-2.6890.19310760.146122691334594
2.689-2.7960.19810590.146122301328994
2.796-2.9240.20310640.149122031326793
2.924-3.0780.19710540.151121371319193
3.078-3.270.19510620.156121711323393
3.27-3.5230.19210700.145121911326193
3.523-3.8770.16410490.138121241317393
3.877-4.4380.16110600.131121101317093
4.438-5.5890.16910710.134123671343894
5.589-41.540.22510140.18116151262989
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.43480.21440.04450.55150.04040.25390.0055-0.02320.0288-0.0112-0.0299-0.0180.0099-0.10840.01470.04930.00530.00480.11950.01850.0654-14.4258-7.1224-37.8421
20.29240.24760.07640.64730.10620.48390.00020.05770.0183-0.0444-0.04760.00410.009-0.17730.0320.05880.0220.00130.15960.0070.0578-14.6235-15.558817.6677
30.3156-0.1542-0.04310.61290.10660.39210.0109-0.0847-0.00980.0346-0.0575-0.0042-0.0047-0.15770.03320.0665-0.01560.00050.1590.00630.052411.0748-30.6967-7.2808
40.3221-0.22860.0130.5130.01340.22390.00080.0164-0.01770.014-0.0223-0.0106-0.0164-0.10940.0110.0585-0.0088-0.00250.12960.01920.076211.2693-22.5917-62.4349
50.7591-0.167-0.07640.36720.21051.2570.0085-0.0222-0.22330.01810.0179-0.0290.25270.1081-0.02170.1360.01360.00310.0643-0.01090.1609-16.7047-55.1105-26.3579
60.8327-0.2173-0.4940.4227-0.07291.32-0.09930.1294-0.1739-0.05540.003-0.01120.3147-0.05760.09390.1563-0.03060.02630.075-0.05140.1568-16.3744-47.2923-80.9918
70.79620.15690.48840.3598-0.0971.3823-0.115-0.13050.17910.04990.0058-0.0179-0.3381-0.06130.10390.16410.0283-0.03450.077-0.05090.16119.34117.5892-19.289
80.77760.13220.04990.3310.18261.27110.00620.02320.217-0.00410.0202-0.0378-0.25870.1057-0.01840.1462-0.0148-0.00220.0634-0.01290.16668.998225.4087-73.9392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 307
2X-RAY DIFFRACTION2chain BB1 - 307
3X-RAY DIFFRACTION3chain KK1 - 2
4X-RAY DIFFRACTION4chain PP1 - 307
5X-RAY DIFFRACTION5chain ZZ1 - 307
6X-RAY DIFFRACTION6chain UU1 - 307
7X-RAY DIFFRACTION7chain ee1 - 307
8X-RAY DIFFRACTION8chain jj1 - 307

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