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- PDB-3q3c: Crystal structure of a serine dehydrogenase from Pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 3q3c
TitleCrystal structure of a serine dehydrogenase from Pseudomonas aeruginosa pao1 in complex with NAD
ComponentsProbable 3-hydroxyisobutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / alpha-beta fold
Function / homology
Function and homology information


L-serine 3-dehydrogenase (NAD+) / 3-hydroxyisobutyrate dehydrogenase activity / branched-chain amino acid catabolic process / L-serine catabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding / protein homotetramerization
Similarity search - Function
3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 ...3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-dependent L-serine dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.299 Å
AuthorsTan, K. / Singer, A.U. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Yakunin, A.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Biochemical and Structural Studies of Uncharacterized Protein PA0743 from Pseudomonas aeruginosa Revealed NAD+-dependent L-Serine Dehydrogenase.
Authors: Tchigvintsev, A. / Singer, A. / Brown, G. / Flick, R. / Evdokimova, E. / Tan, K. / Gonzalez, C.F. / Savchenko, A. / Yakunin, A.F.
History
DepositionDec 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Feb 1, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1572
Polymers31,4941
Non-polymers6631
Water55831
1
A: Probable 3-hydroxyisobutyrate dehydrogenase
hetero molecules

A: Probable 3-hydroxyisobutyrate dehydrogenase
hetero molecules

A: Probable 3-hydroxyisobutyrate dehydrogenase
hetero molecules

A: Probable 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6298
Polymers125,9754
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_554y,x,-z-1/31
crystal symmetry operation10_664-y+1,-x+1,-z-1/31
Buried area17650 Å2
ΔGint-141 kcal/mol
Surface area38930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.724, 92.724, 126.481
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Probable 3-hydroxyisobutyrate dehydrogenase


Mass: 31493.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TEV cleavage / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: PA0743 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3)-RP / References: UniProt: Q9I5I6, EC: 1.1.1.276
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 4 M Ammonium Acetate, 0.1 M sodium acetate pH 4.6 cryoprotected with 12% ethylene glycol and soaked with 10 mM NAD, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2007 / Details: mirrors
RadiationMonochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 15260 / Num. obs: 14802 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Redundancy: 15.16 % / Biso Wilson estimate: 49.84 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 48.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1373 / % possible all: 94

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000ShelxCphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.299→37.391 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2624 750 5.08 %
Rwork0.1912 --
obs0.1945 14766 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.379 Å2 / ksol: 0.297 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.5004 Å20 Å20 Å2
2---1.5004 Å2-0 Å2
3---3.0008 Å2
Refinement stepCycle: LAST / Resolution: 2.299→37.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 44 31 2189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082207
X-RAY DIFFRACTIONf_angle_d1.3282998
X-RAY DIFFRACTIONf_dihedral_angle_d19.403789
X-RAY DIFFRACTIONf_chiral_restr0.08344
X-RAY DIFFRACTIONf_plane_restr0.004389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2993-2.47680.31211480.2632635X-RAY DIFFRACTION96
2.4768-2.7260.33091590.24562771X-RAY DIFFRACTION100
2.726-3.12030.32851680.24252751X-RAY DIFFRACTION100
3.1203-3.93050.25361380.19222850X-RAY DIFFRACTION100
3.9305-37.39550.21241370.15593009X-RAY DIFFRACTION99
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)
13.8271-1.1361-2.77992.8131.92222.6779-1.2920.8161-0.54790.75270.4856-0.17121.02-0.58610.71060.6528-0.27130.13920.4235-0.10450.3148-13.494627.0136-6.4229
24.7532-1.535-2.76763.72490.22994.1361-1.26350.1555-0.58880.12881.07590.53021.5408-0.49530.33751.1778-0.23230.21270.3975-0.12690.4004-16.102422.1307-0.4735
34.33571.5-2.53262.79921.17553.4524-1.12250.186-1.08620.66320.2885-0.51672.3461-0.23060.84891.1168-0.36110.38070.5316-0.12960.6614-8.249819.5649-12.8558
42.30450.4378-0.3011.750.56162.0135-0.94721.3142-0.518-0.09690.08950.151.9427-0.88020.61881.2194-0.65540.36920.7905-0.35280.5095-6.390118.7092-20.7297
52.888-1.5543-0.99421.7128-0.01490.7762-0.29281.15210.27890.32810.1743-0.02890.606-0.78890.08610.4498-0.28840.05940.6156-0.06410.3255-8.426630.4546-19.2842
63.1305-0.8718-1.60430.42810.27622.0120.15921.58030.45290.10180.22620.3646-0.1274-1.4345-0.18790.3949-0.30810.03571.37510.10360.5147-14.904734.3902-21.9092
70.70231.018-1.40320.2586-1.12152.91340.1666-0.1247-0.06180.22590.06780.0491-0.1344-0.4803-0.23850.32110.0305-0.00840.38910.06140.35059.03447.0264-16.6975
81.1862.0723-1.34554.5263-1.70972.0365-0.79430.0776-0.62590.40750.679-0.3413-0.8014-1.0034-0.00780.54960.0890.08660.3749-0.01060.30145.811559.9125-18.2074
90.98110.40110.93681.89240.17591.14680.2051-0.3509-0.16230.12820.15560.17420.0455-0.5326-0.31080.3318-0.0466-0.00980.44270.13270.371610.386840.7468-11.3631
102.42671.3951.28794.7848-2.17032.808-0.0007-1.7011-0.44170.3746-0.4372-0.4917-0.4321-0.24290.31410.4950.0526-0.07680.82830.00650.746219.147749.531-3.0294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:37)
2X-RAY DIFFRACTION2(chain A and resid 38:50)
3X-RAY DIFFRACTION3(chain A and resid 51:73)
4X-RAY DIFFRACTION4(chain A and resid 74:110)
5X-RAY DIFFRACTION5(chain A and resid 111:140)
6X-RAY DIFFRACTION6(chain A and resid 141:160)
7X-RAY DIFFRACTION7(chain A and resid 161:205)
8X-RAY DIFFRACTION8(chain A and resid 206:209)
9X-RAY DIFFRACTION9(chain A and resid 210:291)
10X-RAY DIFFRACTION10(chain A and resid 292:296)

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