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- PDB-4wso: X-ray crystal structure of a nicotinate nucleotide adenylyltransf... -

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Basic information

Entry
Database: PDB / ID: 4wso
TitleX-ray crystal structure of a nicotinate nucleotide adenylyltransferase from Burkholderia thailandensis bound to NAD
ComponentsProbable nicotinate-nucleotide adenylyltransferase
KeywordsTRANSFERASE / SSGCID / nicotinate nucleotide adenylyltransferase / Burkholderia thailandensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Probable nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: to be published
Title: X-ray crystal structure of a nicotinate nucleotide adenylyltransferase from Burkholderia thailandensis bound to NAD
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Fairman, J.W. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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: Probable nicotinate-nucleotide adenylyltransferase
B: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8316
Polymers58,3142
Non-polymers1,5174
Water6,918384
1
A: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9163
Polymers29,1571
Non-polymers7582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9163
Polymers29,1571
Non-polymers7582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.200, 91.320, 60.130
Angle α, β, γ (deg.)90.000, 116.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

21B-431-

HOH

Detailsbiological unit is a monomer

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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: 29157.127 Da / Num. of mol.: 2 / Fragment: ButhA.00448.a.A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: nadD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2SZT3, nicotinate-nucleotide adenylyltransferase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 3.17 Å3/Da / Density % sol: 61.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: JCSG+ C1: 0.1 M sodium phosphate pH 4.2, 0.2 M sodium chloride, 20% PEG 8000; ButhA.00448.a.A1.PS01231 at 20 mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2012
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 37482 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.19 % / Biso Wilson estimate: 19.03 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.117 / Χ2: 0.916 / Net I/σ(I): 10.45 / Num. measured all: 119578
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.05-2.10.820.4772.878827285128260.57299.1
2.1-2.160.8960.4093.168648276827470.48999.2
2.16-2.220.9290.3513.78422268426630.41999.2
2.22-2.290.9150.344.128017263625730.40797.6
2.29-2.370.9540.2644.797908253024990.31698.8
2.37-2.450.9650.2265.767676244324080.2798.6
2.45-2.540.9730.2046.057461238323330.24497.9
2.54-2.650.980.1776.977131227322260.21297.9
2.65-2.760.9840.1527.96834219221310.18197.2
2.76-2.90.9870.1348.916562209320400.15997.5
2.9-3.060.9910.10210.916215199419360.12197.1
3.06-3.240.9940.08213.315834188218130.09896.3
3.24-3.470.9960.06416.515479177916990.07695.5
3.47-3.740.9970.04821.295063167415830.05894.6
3.74-4.10.9960.04822.654568152714400.05894.3
4.1-4.580.9970.03925.854077139413050.04793.6
4.58-5.290.9970.03526.353753120911390.04294.2
5.29-6.480.9970.03724.88325510429680.04392.9
6.48-9.170.9980.03129.4624928107420.03791.6
9.170.9980.02636.0513564684110.03187.8

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXphenix.refine: dev_1810refinement
XSCALEdata scaling
BALBESphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K4M

1k4m


Resolution: 2.05→37.963 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 1905 5.09 %RANDOM
Rwork0.2013 35557 --
obs0.2032 37462 97.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.76 Å2 / Biso mean: 24.649 Å2 / Biso min: 6.06 Å2
Refinement stepCycle: final / Resolution: 2.05→37.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3429 0 98 384 3911
Biso mean--16.34 31.8 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023645
X-RAY DIFFRACTIONf_angle_d0.6785011
X-RAY DIFFRACTIONf_chiral_restr0.027584
X-RAY DIFFRACTIONf_plane_restr0.003642
X-RAY DIFFRACTIONf_dihedral_angle_d13.7361301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.10130.31251320.28172587271999
2.1013-2.15810.28271330.25572585271899
2.1581-2.22160.26971170.24152590270799
2.2216-2.29330.30431750.2462531270698
2.2933-2.37520.26591150.21612581269699
2.3752-2.47030.23641390.22072563270299
2.4703-2.58270.28651360.22062527266398
2.5827-2.71890.27421480.22022568271698
2.7189-2.88920.26271440.22872533267798
2.8892-3.11210.24881410.21372524266597
3.1121-3.42510.221150.19492536265196
3.4251-3.92030.22241070.16892510261795
3.9203-4.93750.18851470.15122475262294
4.9375-37.96910.18581560.16712447260393
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8956-0.89070.05012.4053-0.10841.73030.08260.03220.0663-0.0765-0.0460.0264-0.1585-0.0086-0.01350.1077-0.02530.02340.06750.00140.104731.681350.4911-21.1126
23.3089-1.1697-1.33431.7517-0.68141.5278-0.09230.36390.2244-0.54170.05750.1193-0.0516-0.03760.07580.27640.03240.01270.07710.00330.162531.55250.3344-27.1864
34.1748-1.2331-1.90641.1075-0.68992.98450.48850.6523-0.2681-0.6642-0.3359-0.1113-0.064-0.1015-0.10850.36330.04490.08260.1668-0.03010.190534.095437.6845-30.0503
40.6654-0.6908-0.49843.1759-0.07420.8894-0.0624-0.0174-0.0997-0.0068-0.03830.16750.0823-0.05430.08730.1207-0.00070.01610.1019-0.00920.109131.119637.8755-13.4711
53.62910.55260.22383.40860.76263.7793-0.0555-0.39740.20690.36820.03950.5271-0.3728-0.41430.04090.23690.04880.04490.16230.00010.235321.139366.6172-14.9479
61.9477-0.92741.39643.3138-3.47635.1745-0.07390.0246-0.14470.1260.00290.07070.0137-0.07240.02950.15810.00770.04980.0647-0.03040.117129.915250.453812.1484
71.6818-0.55340.05942.7623-0.17371.4413-0.19530.04580.03010.16220.033-0.2999-0.22850.25790.14660.101-0.01380.01420.0680.00970.116739.359950.558617.2014
87.93591.2724.26046.3258-1.15278.7183-0.10840.0501-0.6984-0.3311-0.0117-0.21760.12490.0680.02940.21180.02070.09930.08220.00980.200741.748339.920614.7688
96.11052.62526.96162.23742.96498.01820.1591-0.1986-0.4844-0.15180.0074-0.39440.2436-0.0203-0.11260.19320.02520.05370.09450.03860.230237.511346.86098.0964
101.8044-0.54313.01673.4666-2.81728.64-0.14470.15230.2879-0.1597-0.2204-0.652-0.21410.3240.36240.2229-0.00880.10580.16750.0620.287643.699360.147810.4339
111.39330.1098-0.70534.1295-0.17262.46090.1097-0.14640.0750.3231-0.1645-0.1312-0.24250.12640.03930.1857-0.00980.01110.10270.01960.135132.923661.007821.2567
120.8840.24841.38350.57261.61895.18170.2612-0.05810.00760.2439-0.08960.12020.1426-0.25220.15970.32510.01150.11750.09280.00850.181525.471466.822316.1426
130.4506-0.19740.00662.0075-0.01450.6424-0.0534-0.1518-0.0538-0.1652-0.03020.04140.0544-0.01050.05250.15240.01140.09560.1370.00010.193224.923456.155617.8341
143.5484-0.20641.92146.66590.54721.1062-0.2359-1.0524-0.63351.70510.28410.7128-0.3405-0.0823-0.11540.42810.10320.10050.3490.1040.269136.33535.250631.8904
150.91080.67150.71175.3467-2.6782.6691-0.3467-0.8128-0.77311.02590.1506-0.090.51860.3624-0.11430.50540.12690.12690.32670.14510.45432.229.474826.6539
168.49660.1995-0.53426.9486-0.28584.3341-0.5104-0.338-0.28760.30650.2504-0.20080.11510.23790.23150.24470.02950.08960.1140.01020.227141.629832.083223.1675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 89 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 113 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 129 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 208 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 209 through 250 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 55 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 56 through 77 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 78 through 91 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 92 through 107 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 108 through 128 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 129 through 172 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 173 through 191 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 192 through 208 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 209 through 221 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 222 through 235 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 236 through 250 )B0

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