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- PDB-5das: Structure of Mycobacterium tuberculosis NadD in complex with NADP... -

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Basic information

Entry
Database: PDB / ID: 5das
TitleStructure of Mycobacterium tuberculosis NadD in complex with NADP, P21212, form 2
ComponentsNicotinate-nucleotide adenylyltransferase
KeywordsTRANSFERASE / Rossman fold
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: 2.2 Å
AuthorsKorotkov, K.V.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R03AI117361 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: Structure of Mycobacterium tuberculosis NadD in complex with NADP, P21212
Authors: Korotkov, K.V.
History
DepositionAug 20, 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
B: Nicotinate-nucleotide adenylyltransferase
C: Nicotinate-nucleotide adenylyltransferase
D: Nicotinate-nucleotide adenylyltransferase
A: Nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3838
Polymers89,4094
Non-polymers2,9744
Water7,206400
1
B: Nicotinate-nucleotide adenylyltransferase
A: Nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1914
Polymers44,7052
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-13 kcal/mol
Surface area17250 Å2
MethodPISA
2
C: Nicotinate-nucleotide adenylyltransferase
D: Nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1914
Polymers44,7052
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-16 kcal/mol
Surface area16320 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10690 Å2
ΔGint-41 kcal/mol
Surface area31190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.820, 156.130, 48.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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 / NaMN adenylyltransferase


Mass: 22352.281 Da / Num. of mol.: 4 / Fragment: Residues 1-192 / Mutation: C188R, C192T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: nadD, Rv2421c, MTCY428.26 / Plasmid: pRSF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: P9WJJ5, 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.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate pH 5.6, 20% isopropanol, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97903 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 4, 2014
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.2→65.08 Å / Num. obs: 46782 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 29.1 Å2 / Rmerge F obs: 0.99 / Rmerge(I) obs: 0.209 / Rrim(I) all: 0.227 / Χ2: 0.955 / Net I/σ(I): 7.97 / Num. measured all: 304725
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.2-2.266.30.8090.9812.1421088339633741.07399.4
2.26-2.320.7570.9212.3622215335033491100
2.32-2.390.8330.6973.1221230319631960.756100
2.39-2.460.8440.6153.5221203318931890.667100
2.46-2.540.8610.5613.8320154302230210.609100
2.54-2.630.9180.4624.5519605295529550.501100
2.63-2.730.9220.4245.1118882289128900.461100
2.73-2.840.9490.3296.118209274027400.357100
2.84-2.970.9620.2866.8317431262826280.311100
2.97-3.110.9740.2318.2216804254125410.251100
3.11-3.280.9820.1919.3416022242924290.208100
3.28-3.480.9850.15711.1814855229922930.17199.7
3.48-3.720.9910.12812.9713842214921480.139100
3.72-4.020.9920.11414.2912867202120170.12599.8
4.02-4.40.9920.09616.3212138187418740.105100
4.4-4.920.9930.08617.5310956170917080.09499.9
4.92-5.680.9910.09516.239480149014900.103100
5.68-6.960.9910.09415.738283131613150.10399.9
6.96-9.840.9940.07318.846253103510320.0899.7
9.840.9960.06719.2732086075930.07497.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALENovember 3, 2014 BUILT=20141118data scaling
PHASER2.5.6phasing
REFMAC5.8.0124refinement
PDB_EXTRACT3.15data extraction
XDSNovember 3, 2014data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S1O

4s1o


Resolution: 2.2→65.08 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2274 / WRfactor Rwork: 0.1839 / FOM work R set: 0.82 / SU B: 6.081 / SU ML: 0.15 / SU R Cruickshank DPI: 0.2438 / SU Rfree: 0.1996 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 2335 5 %RANDOM
Rwork0.1936 ---
obs0.1958 44461 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.54 Å2 / Biso mean: 27.274 Å2 / Biso min: 6.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.51 Å2
Refinement stepCycle: final / Resolution: 2.2→65.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5612 0 192 400 6204
Biso mean--33.64 30.02 -
Num. residues----723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195950
X-RAY DIFFRACTIONr_bond_other_d0.0020.025498
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9618124
X-RAY DIFFRACTIONr_angle_other_deg0.929312606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7765712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.53622.305256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37715898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.061555
X-RAY DIFFRACTIONr_chiral_restr0.0740.2912
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021385
X-RAY DIFFRACTIONr_mcbond_it1.6592.5552881
X-RAY DIFFRACTIONr_mcbond_other1.6552.5542880
X-RAY DIFFRACTIONr_mcangle_it2.7653.8023579
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 167 -
Rwork0.377 3211 -
all-3378 -
obs--99.35 %

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