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- PDB-4g2n: Crystal structure of putative D-isomer specific 2-hydroxyacid deh... -

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Basic information

Entry
Database: PDB / ID: 4g2n
TitleCrystal structure of putative D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding from Polaromonas sp. JS6 66
ComponentsD-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding
Similarity search - Component
Biological speciesPolaromonas sp. JS666 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of putative D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding from Polaromonas sp. JS6 66
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. ...Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C.
History
DepositionJul 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding
B: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding
C: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding
D: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,25312
Polymers152,6294
Non-polymers6238
Water16,700927
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding
C: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5915
Polymers76,3152
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-29 kcal/mol
Surface area25390 Å2
MethodPISA
3
B: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding
D: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6627
Polymers76,3152
Non-polymers3475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-54 kcal/mol
Surface area25140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.431, 68.158, 77.369
Angle α, β, γ (deg.)96.930, 90.680, 94.380
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the same as asym.

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Components

#1: Protein
D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding


Mass: 38157.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas sp. JS666 (bacteria) / Strain: JS6 66 / Gene: Bpro_5114 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q120R1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 927 / 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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.8 M LiCl, 0.1M Tris:HCl, pH 8.5, 32% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 1.9 % / Av σ(I) over netI: 16.32 / Rmerge(I) obs: 0.06 / Χ2: 1.41 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 266267 / % possible obs: 94.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.615092.810.0373.1341.9
3.664.6193.710.0372.7181.8
3.23.6696.210.0412.41.9
2.913.296.910.0462.0141.9
2.72.919710.0551.6681.9
2.542.796.810.0651.5491.9
2.412.5496.810.0761.4191.9
2.312.4196.510.091.3111.9
2.222.3196.310.1081.3191.9
2.142.2296.210.1321.1911.9
2.072.1496.210.1581.141.9
2.022.079610.191.0621.9
1.962.0296.110.2440.9811.9
1.911.9695.910.3020.9261.9
1.871.9195.610.3990.921.9
1.831.8795.710.5010.8461.9
1.791.8395.510.5970.8511.9
1.761.7994.210.6610.8021.8
1.731.7690.710.7380.7791.7
1.71.7377.810.7830.7731.6
ReflectionResolution: 1.7→50 Å / Num. obs: 266267 / % possible obs: 94.6 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.06 / Χ2: 1.406 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.731.60.783109150.773177.8
1.73-1.761.70.738128870.779190.7
1.76-1.791.80.661132040.802194.2
1.79-1.831.90.597133860.851195.5
1.83-1.871.90.501134450.846195.7
1.87-1.911.90.399134440.92195.6
1.91-1.961.90.302134290.926195.9
1.96-2.021.90.244135890.981196.1
2.02-2.071.90.19134751.062196
2.07-2.141.90.158135801.14196.2
2.14-2.221.90.132134791.191196.2
2.22-2.311.90.108135491.319196.3
2.31-2.411.90.09136541.311196.5
2.41-2.541.90.076136111.419196.8
2.54-2.71.90.065135781.549196.8
2.7-2.911.90.055136361.668197
2.91-3.21.90.046136642.014196.9
3.2-3.661.90.041134732.4196.2
3.66-4.611.80.037132152.718193.7
4.61-501.90.037130543.134192.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→19.96 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.2132 / WRfactor Rwork: 0.1869 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8373 / SU B: 5.497 / SU ML: 0.088 / SU R Cruickshank DPI: 0.1181 / SU Rfree: 0.1104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2176 6801 5 %RANDOM
Rwork0.1899 ---
obs0.1913 135460 96.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.11 Å2 / Biso mean: 34.3086 Å2 / Biso min: 16.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.11 Å20.02 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9758 0 38 927 10723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910020
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.97613587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07151285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91622.483439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.379151596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.26815105
X-RAY DIFFRACTIONr_chiral_restr0.0890.21568
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217557
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 430 -
Rwork0.339 8278 -
all-8708 -
obs--84.23 %
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)
10.4435-0.38350.08470.7975-0.05650.0751-0.0139-0.0615-0.06880.0240.05480.1175-0.0102-0.0079-0.04090.0302-0.01450.00050.0450.0230.0408-7.82953.010145.0172
20.9059-0.458-0.16740.55010.63981.00820.05150.07170.0324-0.1304-0.07030.0044-0.1705-0.10580.01880.1956-0.03870.05270.12590.05340.0773-27.232915.137185.0693
30.841-0.59860.03830.7819-0.11540.2341-0.00560.03060.09650.01010.0061-0.1227-0.00790.0167-0.00050.0153-0.0209-0.01140.03620.00660.039120.2457-15.936742.9399
40.2889-0.3113-0.31980.60850.42961.34230.048-0.08390.07860.04060.0987-0.07470.03410.3891-0.14670.114-0.03290.01520.1844-0.0170.03991.3151-2.923983.1326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 324
2X-RAY DIFFRACTION2B6 - 323
3X-RAY DIFFRACTION3C6 - 324
4X-RAY DIFFRACTION4D7 - 323

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