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- PDB-4ina: Crystal Structure of the Q7MSS8_WOLSU protein from Wolinella succ... -

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Basic information

Entry
Database: PDB / ID: 4ina
TitleCrystal Structure of the Q7MSS8_WOLSU protein from Wolinella succinogenes. Northeast Structural Genomics Consortium Target WsR35
Componentssaccharopine dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / Saccharopine Dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich ...Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesWolinella succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.488 Å
AuthorsVorobiev, S. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Q7MSS8_WOLSU protein from Wolinella succinogenes.
Authors: Vorobiev, S. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJan 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Data collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: saccharopine dehydrogenase
B: saccharopine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)93,3222
Polymers93,3222
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-23 kcal/mol
Surface area33070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.639, 95.490, 104.427
Angle α, β, γ (deg.)90.000, 101.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein saccharopine dehydrogenase /


Mass: 46660.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolinella succinogenes (bacteria) / Gene: WS0167 / Plasmid: WsR35-21.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
References: UniProt: Q7MSS8, saccharopine dehydrogenase (NAD+, L-lysine-forming)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 277 K / Method: microbatch crystallization under oil / pH: 6.5
Details: 20% PEG MME 5000, 0.1M BIS-TRIS, pH 6.5, Microbatch crystallization under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. all: 59291 / Num. obs: 57476 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 35.49 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.6
Reflection shellResolution: 2.49→2.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.6 / Num. unique all: 7303 / % possible all: 97.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.488→45.061 Å / Occupancy max: 1 / Occupancy min: 0.55 / SU ML: 0.81 / Cross valid method: THROUGHOUT / σ(F): 0.98 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2909 5.06 %RANDOM
Rwork0.193 ---
obs0.195 57460 96.98 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.83 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 115.53 Å2 / Biso mean: 36.404 Å2 / Biso min: 13.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.298 Å20 Å2-3.636 Å2
2---5.121 Å2-0 Å2
3---3.824 Å2
Refinement stepCycle: LAST / Resolution: 2.488→45.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6272 0 0 146 6418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066412
X-RAY DIFFRACTIONf_angle_d1.2518673
X-RAY DIFFRACTIONf_chiral_restr0.09939
X-RAY DIFFRACTIONf_plane_restr0.0061120
X-RAY DIFFRACTIONf_dihedral_angle_d15.9822383
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.488-2.5280.3771290.3492544267395
2.528-2.5720.41120.3452660277299
2.572-2.6190.3641410.3322720286199
2.619-2.6690.3541500.2982590274099
2.669-2.7240.3321350.2842688282399
2.724-2.7830.2531480.2712650279899
2.783-2.8480.3081420.2482615275799
2.848-2.9190.2521440.2372620276498
2.919-2.9980.3121180.2432691280999
2.998-3.0860.2731470.2252614276198
3.086-3.1850.221410.2012694283599
3.185-3.2990.2031330.1812594272798
3.299-3.4310.2351550.1892637279298
3.431-3.5870.2271520.1912535268797
3.587-3.7760.231310.1772584271596
3.776-4.0130.1691410.1412566270796
4.013-4.3230.1341670.1252522268996
4.323-4.7570.1671200.1222551267195
4.757-5.4440.1741410.152555269695
5.444-6.8550.2191300.1882525265594
6.855-45.0680.1531320.1642396252890
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)
10.59930.03840.19710.6540.10520.4974-0.00190.02110.01240.0243-0.0066-0.01210.0443-0.02190.01350.1709-0.01540.0070.17150.01220.1558-2.73617.36227.0815
20.2458-0.0169-0.06550.58860.00870.69630.00740.01270.00830.0043-0.0094-0.0502-0.03680.03850.00810.1730.00250.00170.207-0.00580.209316.954151.084226.1464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 395
2X-RAY DIFFRACTION2chain BB2 - 403

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