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- PDB-1lw7: NADR PROTEIN FROM HAEMOPHILUS INFLUENZAE -

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Basic information

Entry
Database: PDB / ID: 1lw7
TitleNADR PROTEIN FROM HAEMOPHILUS INFLUENZAE
ComponentsTRANSCRIPTIONAL REGULATOR NADR
KeywordsTRANSFERASE / NAD / NMN / NMN Adenylyl transferase / Ribosylnicotinamide kinase
Function / homology
Function and homology information


ribosylnicotinamide kinase / ribosylnicotinamide kinase activity / nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Nicotinamide-nucleotide adenylyltransferase / NAD biosynthesis/regulator protein NadR / NadR/Ttd14, AAA domain / NadR, nicotinamide/nicotinate mononucleotide adenylyltransferase domain / AAA domain / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleotide triphosphate hydrolases ...Nicotinamide-nucleotide adenylyltransferase / NAD biosynthesis/regulator protein NadR / NadR/Ttd14, AAA domain / NadR, nicotinamide/nicotinate mononucleotide adenylyltransferase domain / AAA domain / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Bifunctional NAD biosynthesis protein NadR
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsSingh, S.K. / Kurnasov, O.V. / Chen, B. / Robinson, H. / Grishin, N.V. / Osterman, A.L. / Zhang, H.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of Haemophilus influenzae NadR protein. A bifunctional enzyme endowed with NMN adenyltransferase and ribosylnicotinimide kinase activities.
Authors: Singh, S.K. / Kurnasov, O.V. / Chen, B. / Robinson, H. / Grishin, N.V. / Osterman, A.L. / Zhang, H.
History
DepositionMay 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATOR NADR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7618
Polymers42,9541
Non-polymers1,8077
Water0
1
A: TRANSCRIPTIONAL REGULATOR NADR
hetero molecules

A: TRANSCRIPTIONAL REGULATOR NADR
hetero molecules

A: TRANSCRIPTIONAL REGULATOR NADR
hetero molecules

A: TRANSCRIPTIONAL REGULATOR NADR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,04432
Polymers171,8164
Non-polymers7,22928
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_765-x+2,-y+1,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+2/31
crystal symmetry operation12_555x,x-y,-z+2/31
Buried area22070 Å2
ΔGint-305 kcal/mol
Surface area60520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)106.871, 106.871, 174.945
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein TRANSCRIPTIONAL REGULATOR NADR


Mass: 42953.898 Da / Num. of mol.: 1 / Fragment: NadR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: NadR / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P44308
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM

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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: 3.3 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.8M Ammonium sulfate, 0.1M MES pH 5.6, Protein Conc. 10 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMHEPES1droppH7.2
30.3 M1dropNaCl
41 mMdithiothreitol1drop
50.1 MMES1reservoirpH6.0
61.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.984 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 20, 2001
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 13327 / Num. obs: 13327 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 137 Å2 / Rsym value: 0.041 / Net I/σ(I): 17.6
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 0.409 / % possible all: 97.3
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 30 Å / % possible obs: 98 % / Num. measured all: 183179 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 97.3 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.9→30 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1284 10.3 %RANDOM
Rwork0.236 ---
all-13327 --
obs-12463 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9 Å2 / ksol: 0.306 e/Å3
Displacement parametersBiso mean: 79.1 Å2
Baniso -1Baniso -2Baniso -3
1-19.99 Å227.08 Å20 Å2
2--19.99 Å20 Å2
3----39.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2842 0 113 0 2955
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.04
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.443 182 10.6 %
Rwork0.384 1530 -
obs-1530 77.4 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.56
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04

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