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- PDB-5deo: Mycobacterium abscessus NadD in complex with nicotinic acid adeni... -

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Basic information

Entry
Database: PDB / ID: 5deo
TitleMycobacterium abscessus NadD in complex with nicotinic acid adenine dinucleotide
ComponentsNicotinate-nucleotide adenylyltransferase
KeywordsTRANSFERASE / Rossman fold / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


nicotinate-nucleotide adenylyltransferase / 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
NICOTINIC ACID ADENINE DINUCLEOTIDE / Probable nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å
AuthorsReed, R.W. / Korotkov, K.V. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R03AI117361 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103486 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110787 United States
CitationJournal: to be published
Title: Mycobacterium abscessus NadD in complex with nicotinic acid adenine dinucleotide
Authors: Reed, R.W. / Korotkov, K.V.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nicotinate-nucleotide adenylyltransferase
B: Nicotinate-nucleotide adenylyltransferase
C: Nicotinate-nucleotide adenylyltransferase
D: Nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7048
Polymers94,0424
Non-polymers2,6624
Water4,017223
1
A: Nicotinate-nucleotide adenylyltransferase
B: Nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3524
Polymers47,0212
Non-polymers1,3312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-15 kcal/mol
Surface area16510 Å2
MethodPISA
2
C: Nicotinate-nucleotide adenylyltransferase
D: Nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3524
Polymers47,0212
Non-polymers1,3312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-17 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.090, 58.438, 109.884
Angle α, β, γ (deg.)90.000, 90.740, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23510.471 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: nadD, MAB_1621 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: B1MMZ4, nicotinate-nucleotide adenylyltransferase
#2: Chemical
ChemComp-DND / NICOTINIC ACID ADENINE DINUCLEOTIDE / DEAMIDO-NAD+


Mass: 665.418 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N6O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris-HCl pH 8.5, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.22→71.08 Å / Num. obs: 43720 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 44.242 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.127 / Χ2: 0.995 / Net I/σ(I): 12.24 / Num. measured all: 164555
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.22-2.283.80.5961.032.2312368330332411.19898.1
2.28-2.340.630.8922.5912139322531661.03898.2
2.34-2.410.6860.7813.0911724311230710.90998.7
2.41-2.480.7470.673.7311619306330230.7898.7
2.48-2.560.8010.5344.5811101293128840.62298.4
2.56-2.650.8710.4145.5110881286628370.48299
2.65-2.750.8840.3835.910373274527070.44698.6
2.75-2.870.910.2987.2310074265526280.34899
2.87-2.990.9560.1999.469564253825020.23298.6
2.99-3.140.9760.15111.089189244124080.17698.6
3.14-3.310.980.11712.998621232022890.13898.7
3.31-3.510.990.0816.437985220421550.09597.8
3.51-3.750.9930.05620.337285206519890.06796.3
3.75-4.050.9950.04623.436614192218110.05594.2
4.05-4.440.9960.03529.096028178516600.04293
4.44-4.960.9960.0333.45459162415080.03692.9
4.96-5.730.9970.0332.84778143113280.03692.8
5.73-7.020.9960.02934.333959121911140.03591.4
7.02-9.930.9980.02439.731299568860.02992.7
9.930.9980.02540.9216655475130.0393.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEVERSION November 3, 2014 BUILT=20141118data scaling
PHASER2.5.7phasing
REFMAC5.8.0124refinement
PDB_EXTRACT3.15data extraction
XDSVERSION November 3, 2014data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YMI

4ymi


Resolution: 2.22→71.08 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2723 / WRfactor Rwork: 0.2261 / FOM work R set: 0.7698 / SU B: 8.675 / SU ML: 0.215 / SU R Cruickshank DPI: 0.3149 / SU Rfree: 0.2448 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.315 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2815 2223 5.1 %RANDOM
Rwork0.234 ---
obs0.2365 41530 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.58 Å2 / Biso mean: 45.08 Å2 / Biso min: 15.82 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20 Å20.16 Å2
2---0.75 Å20 Å2
3----1.03 Å2
Refinement stepCycle: final / Resolution: 2.22→71.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5646 0 176 223 6045
Biso mean--44.98 38.86 -
Num. residues----728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195964
X-RAY DIFFRACTIONr_bond_other_d0.0020.025568
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.9438144
X-RAY DIFFRACTIONr_angle_other_deg0.906312721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0075716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.76721.797256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57515880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6071560
X-RAY DIFFRACTIONr_chiral_restr0.0650.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021426
X-RAY DIFFRACTIONr_mcbond_it2.0944.4162900
X-RAY DIFFRACTIONr_mcbond_other2.0944.4152899
X-RAY DIFFRACTIONr_mcangle_it3.4956.6053604
LS refinement shellResolution: 2.22→2.278 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 149 -
Rwork0.305 3084 -
all-3233 -
obs--98.15 %

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