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- PDB-4s1o: Structure of Mycobacterium tuberculosis NadD in complex with NADP -

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Basic information

Entry
Database: PDB / ID: 4s1o
TitleStructure of Mycobacterium tuberculosis NadD in complex with NADP
ComponentsProbable nicotinate-nucleotide adenylyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


nicotinate-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding
Similarity search - Function
Nicotinate/nicotinamide nucleotide adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / : / Probable nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsKorotkov, K.V.
CitationJournal: To be Published
Title: Structure of Mycobacterium tuberculosis protein
Authors: Korotkov, K.V.
History
DepositionJan 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Other
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable nicotinate-nucleotide adenylyltransferase
B: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2626
Polymers44,7052
Non-polymers1,5584
Water4,324240
1
A: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1313
Polymers22,3521
Non-polymers7792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1313
Polymers22,3521
Non-polymers7792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Probable nicotinate-nucleotide adenylyltransferase
B: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules

A: Probable nicotinate-nucleotide adenylyltransferase
B: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,52512
Polymers89,4094
Non-polymers3,1158
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area11030 Å2
ΔGint-90 kcal/mol
Surface area29020 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-36 kcal/mol
Surface area16280 Å2
MethodPISA
5
A: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules

A: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2626
Polymers44,7052
Non-polymers1,5584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area4040 Å2
ΔGint-27 kcal/mol
Surface area15790 Å2
MethodPISA
6
B: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules

B: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2626
Polymers44,7052
Non-polymers1,5584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area4160 Å2
ΔGint-26 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.060, 66.060, 165.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Probable nicotinate-nucleotide adenylyltransferase / Deamido-NAD(+) diphosphorylase / Deamido-NAD(+) pyrophosphorylase / Nicotinate mononucleotide ...Deamido-NAD(+) diphosphorylase / Deamido-NAD(+) pyrophosphorylase / Nicotinate mononucleotide adenylyltransferase


Mass: 22352.281 Da / Num. of mol.: 2 / Fragment: residues 3-200 / Mutation: C196R, C200T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: LH57_13225, nadD, P425_02519, Rv2421c, RVBD_2421c / Plasmid: pRSF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: I6X474, UniProt: P9WJJ5*PLUS, nicotinate-nucleotide adenylyltransferase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#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.: 240 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT THE SEQUENCE IS MIS-ANNOTATED IN THE DATABASES. THE CORRECT START SEQUENCE ...THE AUTHORS STATE THAT THE SEQUENCE IS MIS-ANNOTATED IN THE DATABASES. THE CORRECT START SEQUENCE IS MHGRRLGVM WHICH WAS CONFIRMED EXPERIMENTALLY.

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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: 47.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M magnesium nitrate, 20% PEG3350, pH 7.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2014
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.84→47.03 Å / Num. all: 37156 / Num. obs: 37134 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 32.415 Å2 / Rmerge(I) obs: 0.09 / Χ2: 1.006 / Net I/σ(I): 13.57
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.84-1.891.0162.291991627091100
1.89-1.940.6573.68191082653199.9
1.94-20.544.041858825311100
2-2.060.3695.641846825081100
2.06-2.120.2936.87175012401199.9
2.12-2.20.2527.671732723461100
2.2-2.280.2538.32159502264199.9
2.28-2.380.16210.991594421601100
2.38-2.480.12713.221565021271100
2.48-2.60.10815.391464519941100
2.6-2.740.09517.721403619261100
2.74-2.910.08219.98132381816199.9
2.91-3.110.07222.491241217151100
3.11-3.360.06324.8114891606199.9
3.36-3.680.06225.671032514781100
3.68-4.110.05727.06950013541100
4.11-4.750.05230.01834512011100
4.75-5.820.05329.52702010351100
5.82-8.230.05228.85469827199.9
8.23-47.030.04828.882850483198.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.68 Å47.07 Å
Translation1.68 Å47.07 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.6phasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
SERGUIdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+27 / Resolution: 1.84→47.03 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.204 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 1835 4.9 %RANDOM
Rwork0.1941 ---
all0.1961 37156 --
obs0.1961 35301 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.49 Å2 / Biso mean: 30.679 Å2 / Biso min: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å20 Å2
2--0.51 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.84→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2709 0 98 240 3047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192877
X-RAY DIFFRACTIONr_bond_other_d0.0020.022635
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.9993933
X-RAY DIFFRACTIONr_angle_other_deg0.95636040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9045339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32222.24125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85515424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0641526
X-RAY DIFFRACTIONr_chiral_restr0.0850.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213153
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02679
X-RAY DIFFRACTIONr_mcbond_it2.1112.7851377
X-RAY DIFFRACTIONr_mcbond_other2.1072.7821376
X-RAY DIFFRACTIONr_mcangle_it3.2614.1431709
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 154 -
Rwork0.286 2546 -
all-2700 -
obs--99.93 %

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