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- PDB-5db4: Mycobacterium abscessus NadD in complex with Mg-ATP, space group I41 -

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Basic information

Entry
Database: PDB / ID: 5db4
TitleMycobacterium abscessus NadD in complex with Mg-ATP, space group I41
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
ADENOSINE-5'-TRIPHOSPHATE / Probable nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 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 Mg-ATP, space group I41
Authors: Reed, R.W. / 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,0846
Polymers47,0212
Non-polymers1,0634
Water2,576143
1
A: Nicotinate-nucleotide adenylyltransferase
hetero molecules

A: Nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0846
Polymers47,0212
Non-polymers1,0634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area3850 Å2
ΔGint-37 kcal/mol
Surface area15980 Å2
MethodPISA
2
B: Nicotinate-nucleotide adenylyltransferase
hetero molecules

B: Nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0846
Polymers47,0212
Non-polymers1,0634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area3800 Å2
ΔGint-32 kcal/mol
Surface area16100 Å2
MethodPISA
3
A: Nicotinate-nucleotide adenylyltransferase
B: Nicotinate-nucleotide adenylyltransferase
hetero molecules

A: Nicotinate-nucleotide adenylyltransferase
B: Nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,16812
Polymers94,0424
Non-polymers2,1268
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area10190 Å2
ΔGint-77 kcal/mol
Surface area29530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.098, 67.098, 229.538
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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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.: 2
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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 0.02M HEPES pH 7.6, 14% PEG3350, 0.002M Mg-ATP

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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: Apr 18, 2015
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→57.38 Å / Num. obs: 22829 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 54.114 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.075 / Χ2: 1.036 / Net I/σ(I): 16.8 / Num. measured all: 118283
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
2.28-2.345.20.6111.041.698828172016971.15598.7
2.34-2.40.7370.8292.188557166116370.9298.6
2.4-2.470.8010.6642.778258160115810.73798.8
2.47-2.550.9010.4773.738092156515460.5398.8
2.55-2.630.9230.3674.827962154215260.40899
2.63-2.730.9390.3035.77431143614210.33699
2.73-2.830.9610.247.247427144114280.26799.1
2.83-2.940.980.1699.947005136113490.18799.1
2.94-3.070.9880.12613.146755130512960.13999.3
3.07-3.220.9930.09716.466343123412240.10899.2
3.22-3.40.9960.07121.796143119411880.07999.5
3.4-3.610.9970.05327.375765112311170.05999.5
3.61-3.850.9980.04631.565330104210370.05199.5
3.85-4.160.9990.03835.95507510019970.04399.6
4.16-4.560.9980.03441.0946539159100.03899.5
4.56-5.10.9990.03142.4840758048010.03599.6
5.1-5.890.9990.03341.9937727397360.03699.6
5.89-7.210.9990.03143.4530836076020.03499.2
7.21-10.20.9990.02649.4924324774740.02999.4
10.20.9990.02652.2212972672620.02998.1

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4ymi


Resolution: 2.28→57.38 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2418 / WRfactor Rwork: 0.1856 / FOM work R set: 0.7878 / SU B: 8.254 / SU ML: 0.189 / SU R Cruickshank DPI: 0.245 / SU Rfree: 0.2127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 1139 5 %RANDOM
Rwork0.1934 ---
obs0.1961 21694 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.63 Å2 / Biso mean: 55.888 Å2 / Biso min: 31.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2--1.24 Å20 Å2
3----2.47 Å2
Refinement stepCycle: final / Resolution: 2.28→57.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2735 0 64 143 2942
Biso mean--41.9 50.89 -
Num. residues----354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192858
X-RAY DIFFRACTIONr_bond_other_d0.0020.022685
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9573900
X-RAY DIFFRACTIONr_angle_other_deg0.90236132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2225347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.41121.707123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72715428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9421530
X-RAY DIFFRACTIONr_chiral_restr0.0680.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02675
X-RAY DIFFRACTIONr_mcbond_it2.895.4851409
X-RAY DIFFRACTIONr_mcbond_other2.8895.4831408
X-RAY DIFFRACTIONr_mcangle_it4.5858.1941749
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 85 -
Rwork0.36 1610 -
all-1695 -
obs--98.66 %

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