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

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Basic information

Entry
Database: PDB / ID: 4ybr
TitleStructure of Mycobacterium tuberculosis NadD in complex with NADP, P21212
ComponentsNicotinate-nucleotide adenylyltransferase
KeywordsTRANSFERASE / Rossman fold
Function / homology
Function and homology information


nicotinamide-nucleotide adenylyltransferase activity / 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
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: 1.65 Å
AuthorsKorotkov, K.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103486 United States
CitationJournal: to be published
Title: Structure of Mycobacterium tuberculosis NadD in complex with NADP, P21212
Authors: Korotkov, K.V.
History
DepositionFeb 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 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 2.0Dec 25, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_target_identifier / _pdbx_audit_support.funding_organization
Revision 2.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,93110
Polymers44,7052
Non-polymers2,2268
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-54 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.040, 141.430, 63.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2 / Fragment: residues 3-200 / Mutation: C196R, C200T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (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

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Non-polymers , 5 types, 347 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.87 / Details: 0.1M HEPES pH 7.5, 1.26M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97903 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: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.65→70.71 Å / Num. all: 53894 / Num. obs: 53277 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 28.953 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.071 / Χ2: 1.021 / Net I/σ(I): 16.45 / Num. measured all: 295263
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
1.65-1.744.70.6020.8232.1914630395034440.99992.4
1.69-1.740.7430.772.4819459383337510.85797.9
1.74-1.790.8210.6033.4821082368036800.664100
1.79-1.840.8990.4684.2820821363536340.515100
1.84-1.90.9350.3765.2920312353535330.41599.9
1.9-1.970.9580.287.0519570340634060.308100
1.97-2.050.9770.2019.2718883329332920.221100
2.05-2.130.9870.15112.0418157316731660.166100
2.13-2.220.9890.12813.4217550305330530.141100
2.22-2.330.9930.10415.6216774291529150.115100
2.33-2.460.9950.07920.1215865278027790.087100
2.46-2.610.9960.06822.4214959261726170.075100
2.61-2.790.9980.05525.4314072248424840.061100
2.79-3.010.9980.04629.4113220234523430.05199.9
3.01-3.30.9980.03935.2311907213421320.04399.9
3.3-3.690.9990.03340.8510866195519540.03699.9
3.69-4.260.9990.0344.439592174017390.03399.9
4.26-5.210.9990.02947.758073148514840.03299.9
5.21-7.370.9980.0345.136194118611850.03499.9
7.370.9980.0345.3532777016850.03497.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S1O

4s1o


Resolution: 1.65→70.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2168 / WRfactor Rwork: 0.1873 / FOM work R set: 0.8446 / SU B: 2.137 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1005 / SU Rfree: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 2656 5 %RANDOM
Rwork0.1898 ---
obs0.1911 53277 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.45 Å2 / Biso mean: 25.641 Å2 / Biso min: 11.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.64 Å20 Å2
3---0.74 Å2
Refinement stepCycle: final / Resolution: 1.65→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3069 0 138 339 3546
Biso mean--32.76 35.34 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193333
X-RAY DIFFRACTIONr_bond_other_d0.0020.023086
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9554566
X-RAY DIFFRACTIONr_angle_other_deg0.93937096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7045410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67722.361144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.56215509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2151531
X-RAY DIFFRACTIONr_chiral_restr0.0810.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213876
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02779
X-RAY DIFFRACTIONr_mcbond_it1.5332.2991589
X-RAY DIFFRACTIONr_mcbond_other1.5282.2971588
X-RAY DIFFRACTIONr_mcangle_it2.4333.4271983
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 172 -
Rwork0.315 3265 -
all-3437 -
obs--87.1 %

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