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- PDB-3h2s: Crystal Structure of the Q03B84 Protein from Lactobacillus casei.... -

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Basic information

Entry
Database: PDB / ID: 3h2s
TitleCrystal Structure of the Q03B84 Protein from Lactobacillus casei. Northeast Structural Genomics Consortium Target LcR19.
ComponentsPutative NADH-flavin reductase
KeywordsOXIDOREDUCTASE / Q03B84 / NADH-flavin reductase / NESG / LcR19 / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
: / NAD(P)H-binding / NAD(P)-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
Chem-NDP / NADH-flavin reductase
Similarity search - Component
Biological speciesLactobacillus casei ATCC 334 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsVorobiev, S. / Lew, S. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J. / Nair, R. ...Vorobiev, S. / Lew, S. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J. / Nair, R. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Q03B84 protein from Lactobacillus casei.
Authors: Vorobiev, S. / Lew, S. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J. / Nair, R. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionApr 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative NADH-flavin reductase
B: Putative NADH-flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2844
Polymers48,7932
Non-polymers1,4912
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-7.2 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.664, 93.768, 102.549
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsDIMER ACCORDING TO AGGREGATION SCREENING: 46.96 KDA, 96.9%

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Components

#1: Protein Putative NADH-flavin reductase


Mass: 24396.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei ATCC 334 (bacteria)
Gene: LSEI_0698 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q03B84
#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.: 360 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.2M Potassium nitrate, 1mM NADPH, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 2, 2009
RadiationMonochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 80385 / Num. obs: 80385 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 25.2
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 4.6 / Num. unique all: 8596 / % possible all: 78.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.365 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2131 5 %RANDOM
Rwork0.193 ---
obs0.196 42277 93.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.052 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 0 96 360 3689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223407
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9984671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0135430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76923.676136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70515497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5591522
X-RAY DIFFRACTIONr_chiral_restr0.0820.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022560
X-RAY DIFFRACTIONr_nbd_refined0.2250.21627
X-RAY DIFFRACTIONr_nbtor_refined0.3210.22313
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2318
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.210
X-RAY DIFFRACTIONr_mcbond_it3.2851.52194
X-RAY DIFFRACTIONr_mcangle_it4.24323430
X-RAY DIFFRACTIONr_scbond_it7.09131359
X-RAY DIFFRACTIONr_scangle_it9.2294.51241
LS refinement shellResolution: 1.78→1.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 120 -
Rwork0.204 2366 -
obs-2486 76.59 %
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)
10.1151-0.0276-0.04890.1605-0.05750.1262-0.0082-0.00450.01210.0050.00130.0069-0.0096-0.01110.0068-0.0088-0.0019-0.0021-0.0044-0.0032-0.003119.67950.30442.676
20.191-0.0369-0.01140.18560.0830.1973-0.00910.01410.0029-0.00560.0004-0.0123-0.01630.01320.0087-0.0114-0.0029-0.0026-0.0061-0.0006-0.004228.02650.17311.872
34.6015-4.00751.03464.9455-0.41880.39240.08780.0367-0.0428-0.163-0.13020.0404-0.05870.04780.0423-0.0102-0.0176-0.0023-0.0092-0.0045-0.037826.9546.09845.476
42.72043.37831.41554.87981.56330.79190.04370.0039-0.05220.1683-0.00170.09430.00370.0374-0.0419-0.0071-0.00020.0127-0.00160.0104-0.012920.70146.0519.231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 216
2X-RAY DIFFRACTION2B1 - 216
3X-RAY DIFFRACTION3A301
4X-RAY DIFFRACTION4L - A302

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