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- PDB-3lf2: NADPH Bound Structure of the Short Chain Oxidoreductase Q9HYA2 fr... -

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Basic information

Entry
Database: PDB / ID: 3lf2
TitleNADPH Bound Structure of the Short Chain Oxidoreductase Q9HYA2 from Pseudomonas aeruginosa PAO1 Containing an Atypical Catalytic Center
ComponentsShort Chain OxidoReductase Q9HYA2
KeywordsOXIDOREDUCTASE / sdr / SCOR / Rossmann Fold
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / antibiotic biosynthetic process / NADP binding / metal ion binding
Similarity search - Function
: / short chain dehydrogenase / 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
Chem-NDP / Probable short-chain dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsHuether, R. / Umland, T.C. / Duax, W.L.
CitationJournal: Protein Sci. / Year: 2010
Title: The short-chain oxidoreductase Q9HYA2 from Pseudomonas aeruginosa PAO1 contains an atypical catalytic center.
Authors: Huether, R. / Mao, Q. / Duax, W.L. / Umland, T.C.
History
DepositionJan 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 2013Group: Non-polymer description
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Short Chain OxidoReductase Q9HYA2
B: Short Chain OxidoReductase Q9HYA2
C: Short Chain OxidoReductase Q9HYA2
D: Short Chain OxidoReductase Q9HYA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,06013
Polymers114,0864
Non-polymers1,9749
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16030 Å2
ΔGint-143 kcal/mol
Surface area38100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.788, 112.607, 136.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Short Chain OxidoReductase Q9HYA2


Mass: 28521.584 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3507 / Plasmid: pETSumo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9HYA2

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Non-polymers , 5 types, 466 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM Mes, 100mM MnSO4, 20%(v/v) GLYCEROL 15%(w/v) PEG 4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979454 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979454 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. all: 70279 / Num. obs: 61424 / % possible obs: 87.4 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 30.14 Å2 / Rsym value: 0.067 / Χ2: 1.294 / Net I/σ(I): 9.8
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.58 / Num. unique all: 3574 / Rsym value: 0.499 / Χ2: 1.275 / % possible all: 51.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.91
Highest resolutionLowest resolution
Rotation2.5 Å32.89 Å
Translation2.5 Å32.89 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3LF1

3lf1


Resolution: 2.3→32.894 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.3 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2146 5.05 %random
Rwork0.173 ---
obs0.176 42509 92.72 %-
all-45856 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.233 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 130.38 Å2 / Biso mean: 42.425 Å2 / Biso min: 13.46 Å2
Baniso -1Baniso -2Baniso -3
1-16.674 Å2-0 Å2-0 Å2
2---5.102 Å2-0 Å2
3----11.572 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7869 0 79 457 8405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078113
X-RAY DIFFRACTIONf_angle_d0.99111019
X-RAY DIFFRACTIONf_chiral_restr0.0631261
X-RAY DIFFRACTIONf_plane_restr0.0041437
X-RAY DIFFRACTIONf_dihedral_angle_d16.2282932
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.3530.251110.18722452356224578
2.353-2.4120.3041140.18423022416230281
2.412-2.4770.2821330.1924082541240884
2.477-2.550.2431510.17425262677252688
2.55-2.6330.2521280.17726522780265292
2.633-2.7270.311540.18326772831267794
2.727-2.8360.2761550.19126852840268594
2.836-2.9650.261520.19227712923277196
2.965-3.1210.2591640.18527682932276897
3.121-3.3160.2741580.18427952953279597
3.316-3.5720.2371290.17128462975284698
3.572-3.9310.2361390.15328993038289998
3.931-4.4990.1841460.14628963042289698
4.499-5.6630.2051540.15828983052289898
5.663-32.8980.2021580.17429953153299596
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)
10.08580.0399-0.29870.7103-0.30071.0067-0.0104-0.0436-0.08090.0273-0.0565-0.04430.05190.13760.06060.07880.015-0.0250.11970.02960.1374-32.316638.444-53.9168
20.6935-0.3259-0.08320.2392-0.0980.91280.05140.1247-0.0762-0.0696-0.0960.019-0.0129-0.06420.03580.14220.03150.00040.1364-0.04630.137-39.928143.1298-87.0093
30.77950.08830.08130.5019-0.17150.47950.01130.06750.0923-0.0655-0.0707-0.0157-0.33180.08660.04120.2905-0.0535-0.00860.14790.0370.1413-29.177771.5721-83.461
40.6353-0.0183-0.2030.08040.07661.02890.01-0.08480.05420.0394-0.04730.0077-0.48610.0470.03940.331-0.0445-0.04320.1338-0.01880.1391-38.048168.1041-50.4261
51.01550.5355-0.02510.28540.01070.24010.23560.07770.01490.22580.06790.20570.05570.0082-0.27550.63040.16240.04330.39020.06190.5937-28.310929.2961-54.0703
60.08720.1102-0.01580.138-0.01840.00230.1237-0.0824-0.02720.038-0.0111-0.0303-0.02480.0909-0.06370.8754-0.27860.01120.7763-0.0280.7061-25.18280.4582-82.8694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3
2X-RAY DIFFRACTION2chain BB3 - 265
3X-RAY DIFFRACTION3chain CC5 - 4
4X-RAY DIFFRACTION4chain DD4 - 265
5X-RAY DIFFRACTION5chain EA1 - 266
6X-RAY DIFFRACTION6chain FC1 - 266

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