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- PDB-4rl6: Crystal Structure of the Q04L03_STRP2 protein from Streptococcus ... -

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Basic information

Entry
Database: PDB / ID: 4rl6
TitleCrystal Structure of the Q04L03_STRP2 protein from Streptococcus pneumoniae. Northeast Structural Genomics Consortium Target SpR105
ComponentsSaccharopine dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Q04L03_STRP2 / SpR105
Function / homology
Function and homology information


saccharopine dehydrogenase (NAD+, L-lysine-forming) / saccharopine dehydrogenase (NAD+, L-lysine-forming) activity / nucleotide binding
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
Chem-NDP / Saccharopine dehydrogenase / Saccharopine dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.79 Å
AuthorsVorobiev, S. / Neely, H.M. / Odukwe, C.D. / Seetharaman, J. / Mao, L. / Xiao, R. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. ...Vorobiev, S. / Neely, H.M. / Odukwe, C.D. / Seetharaman, J. / Mao, L. / 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 Q04L03_STRP2 protein from Streptococcus pneumoniae.
Authors: Vorobiev, S. / Neely, H.M. / Odukwe, C.D. / Seetharaman, J. / Mao, L. / Xiao, R. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Saccharopine dehydrogenase
B: Saccharopine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5914
Polymers97,1002
Non-polymers1,4912
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-20 kcal/mol
Surface area33600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.705, 120.845, 154.042
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Saccharopine dehydrogenase


Mass: 48550.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: D39/NCTC 7466 / Gene: lys1, SPD_0812 / Plasmid: SpR105-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
References: UniProt: Q04L03, UniProt: A0A0H2ZP94*PLUS, saccharopine dehydrogenase (NAD+, L-lysine-forming)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 277 K / Method: microbatch under parafin oil / pH: 7
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 5mM NADPH, 10mM Tris-HCl (pH 7.5). Crystallization solution: 40% PEG 4000, 0.1M lithium sulfate, 0.1M MOPS, pH 7.0, microbatch under ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 5mM NADPH, 10mM Tris-HCl (pH 7.5). Crystallization solution: 40% PEG 4000, 0.1M lithium sulfate, 0.1M MOPS, pH 7.0, microbatch under parafin oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.96761 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 5, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96761 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 48128 / Num. obs: 48128 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 64.73 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 17.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.989 / Mean I/σ(I) obs: 1.95 / Num. unique all: 4801 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.9_1692refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.79→49.077 Å / Occupancy max: 1 / Occupancy min: 0.73 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2450 5.1 %RANDOM
Rwork0.179 ---
obs0.18 48061 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.7 Å2 / Biso mean: 66.529 Å2 / Biso min: 24.38 Å2
Refinement stepCycle: LAST / Resolution: 2.79→49.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6368 0 96 47 6511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086616
X-RAY DIFFRACTIONf_angle_d1.5678995
X-RAY DIFFRACTIONf_chiral_restr0.107996
X-RAY DIFFRACTIONf_plane_restr0.0071134
X-RAY DIFFRACTIONf_dihedral_angle_d14.2322404
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.79-2.8430.3121210.2542441256295
2.843-2.9010.2891280.2525022630100
2.901-2.9640.2371600.24225712731100
2.964-3.0330.2811200.24225182638100
3.033-3.1090.2451270.24525532680100
3.109-3.1930.241340.21725782712100
3.193-3.2870.2791370.20525192656100
3.287-3.3930.2621320.19825442676100
3.393-3.5150.2051580.18625172675100
3.515-3.6550.1961290.18325422671100
3.655-3.8220.2281440.16925572701100
3.822-4.0230.2031500.16225092659100
4.023-4.2750.1781270.14925632690100
4.275-4.6050.1541310.13425262657100
4.605-5.0680.1431460.13425532699100
5.068-5.80.1941260.16625512677100
5.8-7.3040.1931510.19525252676100
7.304-49.0840.1991290.18325422671100

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