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- PDB-4b79: THE AEROPATH PROJECT AND PSEUDOMONAS AERUGINOSA HIGH-THROUGHPUT C... -

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Basic information

Entry
Database: PDB / ID: 4b79
TitleTHE AEROPATH PROJECT AND PSEUDOMONAS AERUGINOSA HIGH-THROUGHPUT CRYSTALLOGRAPHIC STUDIES FOR ASSESSMENT OF POTENTIAL TARGETS IN EARLY STAGE DRUG DISCOVERY.
ComponentsPROBABLE SHORT-CHAIN DEHYDROGENASE
KeywordsOXIDOREDUCTASE / INFECTIOUS DISEASE / STRUCTURE-BASED INHIBITOR DESIGN
Function / homology
Function and homology information


fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Probable short-chain dehydrogenase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsMoynie, L. / McMahon, S.A. / Alphey, M.S. / Liu, H. / Duthie, F. / Naismith, J.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: The Aeropath Project Targeting Pseudomonas Aeruginosa: Crystallographic Studies for Assessment of Potential Targets in Early-Stage Drug Discovery
Authors: Moynie, L. / Schnell, R. / Mcmahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M.S. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / ...Authors: Moynie, L. / Schnell, R. / Mcmahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M.S. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / Naismith, J.H. / Schneider, G.
History
DepositionAug 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PROBABLE SHORT-CHAIN DEHYDROGENASE
B: PROBABLE SHORT-CHAIN DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7374
Polymers51,4112
Non-polymers1,3272
Water3,189177
1
A: PROBABLE SHORT-CHAIN DEHYDROGENASE
B: PROBABLE SHORT-CHAIN DEHYDROGENASE
hetero molecules

A: PROBABLE SHORT-CHAIN DEHYDROGENASE
B: PROBABLE SHORT-CHAIN DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,4758
Polymers102,8214
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area17320 Å2
ΔGint-124.5 kcal/mol
Surface area31910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.910, 103.910, 205.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein PROBABLE SHORT-CHAIN DEHYDROGENASE / PA4098


Mass: 25705.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q9HWT0
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 3.13 Å3/Da / Density % sol: 60.6 % / Description: NONE
Crystal growpH: 5
Details: 1.56M SODIUM ACETATE, 0.1M AMMONIUM TARTATE, 3.2% BUTANEDIOL, 0.1M SODIUM ACETATE PH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.98→67.7 Å / Num. obs: 44233 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 12.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.7
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 4.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AVY

4avy


Resolution: 1.98→67.7 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.186 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.21336 2354 5.1 %RANDOM
Rwork0.19262 ---
obs0.19364 44233 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.394 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.98→67.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3523 0 88 177 3788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193686
X-RAY DIFFRACTIONr_bond_other_d0.0030.022475
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9955016
X-RAY DIFFRACTIONr_angle_other_deg1.02335967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2235467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14322.39159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70515569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5321542
X-RAY DIFFRACTIONr_chiral_restr0.0750.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214156
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02800
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.976→2.028 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 179 -
Rwork0.236 2848 -
obs--99.47 %
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)
12.1559-1.4565-1.15453.8861-0.7341.4442-0.2041-0.3817-0.32150.46120.13690.2003-0.05860.16280.06720.179-0.0438-0.00870.35760.25610.2781-8.045-58.43226.151
24.16220.2583-1.21720.5454-0.1391.24070.0674-0.3494-0.63710.04870.0007-0.03450.28560.0799-0.06810.1222-0.0091-0.06230.17750.12560.3834-2.531-65.92810.551
31.1897-0.1186-0.65030.4421-0.07911.02960.0301-0.0926-0.28040.01960.003-0.01290.0118-0.028-0.03310.0704-0.0087-0.00990.22120.04750.2465-4.712-56.2827.906
43.91840.43672.05480.85150.4941.65160.0131-0.1641-0.29240.07710.0230.09860.04450.0142-0.03610.06090.00610.01690.23420.05610.2273-8.63-51.05910.377
52.42854.642.34649.38084.72562.38320.2361-0.0611-0.72830.12130.4178-1.38650.06230.1508-0.65390.1518-0.1666-0.07170.62730.05550.318315.958-44.50817.414
60.7940.34440.20380.69650.39870.81110.0598-0.1154-0.05190.1462-0.02950.0076-0.0582-0.0215-0.03030.10630.00780.01790.27020.03720.1517-4.771-44.28916.101
70.7854-0.5858-0.40920.68550.20671.08110.0474-0.17030.20680.06250.02870.0234-0.1189-0.0405-0.07610.15560.01930.07830.2674-0.08670.2116-12.336-21.26721.004
80.6402-0.18-0.38070.10540.31132.21130.12450.01260.1941-0.0078-0.04730.0063-0.1029-0.0809-0.07720.11520.0090.05150.2272-0.00040.2144-5.499-22.9634.577
92.55571.02740.63530.60960.26851.00710.0851-0.10260.12040.0326-0.08660.0351-0.0570.04540.00150.10090.0050.02590.2556-0.0160.1685-1.464-31.01112.357
1073.573624.5826110.40868.348736.9642165.9719-2.53770.67971.9742-0.6769-0.14880.7108-3.29840.93662.68651.60850.00540.28641.26530.12261.5318-25.075-27.7211.124
1121.932-15.1121-1.88716.8432-5.21346.80970.89391.3629-0.0516-0.8319-0.3640.38170.1106-0.7264-0.530.09530.0750.00840.39350.01550.4436-23.297-37.334-6.418
121.20250.71470.70680.50520.4321.19680.0095-0.0933-0.00970.0444-0.02250.10630.0439-0.02990.0130.09790.01780.0280.2597-0.00120.1746-12.245-38.61911.69
130.1655-1.3574-0.111312.96410.71240.11180.0550.05430.0316-0.22820.06160.1711-0.0896-0.0439-0.11660.13670.02790.08990.3191-0.00960.2678-14.742-23.3097.985
141.2558-0.50872.16660.2327-0.93573.8788-0.001-0.1122-0.25390.10450.19520.0545-0.2868-0.2836-0.19420.20890.2105-0.04820.35570.07750.34612.744-59.03316.576
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 61
2X-RAY DIFFRACTION2A62 - 105
3X-RAY DIFFRACTION3A106 - 157
4X-RAY DIFFRACTION4A158 - 182
5X-RAY DIFFRACTION5A188 - 206
6X-RAY DIFFRACTION6A207 - 241
7X-RAY DIFFRACTION7B1 - 88
8X-RAY DIFFRACTION8B89 - 152
9X-RAY DIFFRACTION9B153 - 181
10X-RAY DIFFRACTION10B182 - 189
11X-RAY DIFFRACTION11B190 - 200
12X-RAY DIFFRACTION12B201 - 241
13X-RAY DIFFRACTION13B1242
14X-RAY DIFFRACTION14A1242

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