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- PDB-4xfd: Crystal Structure of a NH(3)-dependent NAD(+) synthetase from Pse... -

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Basic information

Entry
Database: PDB / ID: 4xfd
TitleCrystal Structure of a NH(3)-dependent NAD(+) synthetase from Pseudomonas aeruginosa
ComponentsNH(3)-dependent NAD(+) synthetase
KeywordsLIGASE / cofactor biosynthesis / ATP-binding / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
NH(3)-dependent NAD(+) synthetase / NAD(+) synthetase / NAD/GMP synthase / NAD synthase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NH(3)-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a NH(3)-dependent NAD(+) synthetase from Pseudomonas aeruginosa
Authors: Dranow, D.M. / Lorimer, D. / Edwards, T.E.
History
DepositionDec 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NH(3)-dependent NAD(+) synthetase


Theoretical massNumber of molelcules
Total (without water)30,7631
Polymers30,7631
Non-polymers00
Water5,567309
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.980, 41.690, 64.470
Angle α, β, γ (deg.)90.000, 113.400, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

21A-385-

HOH

31A-431-

HOH

Detailsbiological unit is a dimertetramer, same as the asymmetric unit

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Components

#1: Protein NH(3)-dependent NAD(+) synthetase


Mass: 30762.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: nadE, PA4920 / Plasmid: PsaeA.00025.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HUP3, NAD+ synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus (B4): 12.5% PEG-1000, 12.5% PEG-3350, 12.5% MPD, 0.1M MES/imidazole, pH 6.5, 0.03M each sodium fluoride, sodium bromide, sodium iodide; PsaeA.00025.a.B1.PW37555 at 23.5 mg/ml, tray 258195b4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 17, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 39807 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 15.51 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.073 / Χ2: 1.035 / Net I/σ(I): 13.03 / Num. measured all: 141766
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
1.55-1.590.8640.5362.7610521292129170.63399.9
1.59-1.630.910.4293.2910364288228780.50599.9
1.63-1.680.9260.3733.879968276427560.43999.7
1.68-1.730.9480.3014.689819271227100.35599.9
1.73-1.790.9670.2395.799573264726420.28299.8
1.79-1.850.9790.18979045250324990.22299.8
1.85-1.920.9860.1588.258883245724450.18699.5
1.92-20.990.11910.438601238123730.1499.7
2-2.090.9920.09712.748153227422660.11499.6
2.09-2.190.9930.08114.817837217821710.09599.7
2.19-2.310.9940.06817.427271204320340.0899.6
2.31-2.450.9950.0619.096928196719560.07199.4
2.45-2.620.9970.05121.416445183518250.0699.5
2.62-2.830.9970.04923.165886170216960.05899.6
2.83-3.10.9970.04225.435416158215740.0599.5
3.1-3.470.9970.03927.254881144914410.04699.4
3.47-40.9970.03629.44261127912600.04298.5
4-4.90.9980.03230.863684108410790.03899.5
4.9-6.930.9980.03129.9528998548500.03699.5
6.930.9980.02629.4613314894350.03289

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→31.642 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1993 1834 4.92 %
Rwork0.1687 35426 -
obs0.1702 37260 93.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.73 Å2 / Biso mean: 24.5564 Å2 / Biso min: 8.15 Å2
Refinement stepCycle: final / Resolution: 1.55→31.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 0 309 2273
Biso mean---34.73 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122061
X-RAY DIFFRACTIONf_angle_d1.2292809
X-RAY DIFFRACTIONf_chiral_restr0.064322
X-RAY DIFFRACTIONf_plane_restr0.007383
X-RAY DIFFRACTIONf_dihedral_angle_d13.884770
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.59190.34191230.28192388251182
1.5919-1.63880.34251280.25352448257685
1.6388-1.69160.26131280.22652535266386
1.6916-1.75210.22571090.20092578268788
1.7521-1.82220.22381310.19542639277091
1.8222-1.90520.23211390.19262703284293
1.9052-2.00560.19031580.17652750290896
2.0056-2.13120.18991580.15892835299397
2.1312-2.29570.17831340.15482886302098
2.2957-2.52670.19951580.16082849300799
2.5267-2.89210.19931610.16252899306099
2.8921-3.64290.17641530.15382956310999
3.6429-31.64810.17991540.15252960311498
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)
15.938-0.35973.33653.70291.80335.26640.4009-0.3834-0.70030.0468-0.4588-00.5295-0.00130.00050.27370.03790.01410.17140.05470.1895-5.559-21.6917.9766
21.28220.6401-0.16744.4906-3.22782.5695-0.0085-0.388-0.1639-0.02470.11790.00160.4059-0.028-0.03770.12960.0261-0.02350.19820.03560.123415.7021-11.766314.5429
34.2318-0.4795-0.87291.76830.33652.36050.0633-0.45040.20380.0731-0.0162-0.12550.03260.1355-0.04120.1224-0.0167-0.01690.1614-0.04480.127717.0744-0.750914.0453
44.0401-3.4565-0.3064.4368-0.25741.768-0.1479-0.35370.62510.2110.104-0.0411-0.2059-0.012-0.05350.171-0.0097-0.01440.1701-0.10450.237115.42057.186511.5844
50.06870.10270.29172.025-1.06632.4257-0.0488-0.58650.40720.4050.11070.0558-0.2743-0.1506-0.05770.22820.00420.0070.3176-0.13410.230210.83910.511118.043
61.48781.90530.19542.7721.12962.35670.07880.04930.5094-0.1596-0.05770.1158-0.3374-0.22960.07010.18570.05540.01890.11280.02470.3344-10.291416.86240.7095
70.6336-0.19190.0140.2977-0.27060.66730.0398-0.19330.15810.01650.00930.0837-0.039-0.003-0.05390.1161-0.0109-0.0030.0878-0.02230.12650.66591.3118.1368
82.96571.31530.6292.03850.10840.76340.0688-0.72270.31040.166-0.06830.1904-0.2170.21380.03670.23910.00050.00630.3833-0.04890.13664.2819-3.849226.5848
91.29290.5028-0.26380.9239-0.67722.9153-0.0173-0.13650.0430.03080.02570.13480.2147-0.2035-0.00710.1360.01790.00440.11750.00530.1172-10.1331-12.346114.3805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -4:20 )A-4 - 20
2X-RAY DIFFRACTION2( CHAIN A AND RESID 21:42 )A21 - 42
3X-RAY DIFFRACTION3( CHAIN A AND RESID 43:75 )A43 - 75
4X-RAY DIFFRACTION4( CHAIN A AND RESID 76:91 )A76 - 91
5X-RAY DIFFRACTION5( CHAIN A AND RESID 92:115 )A92 - 115
6X-RAY DIFFRACTION6( CHAIN A AND RESID 116:133 )A116 - 133
7X-RAY DIFFRACTION7( CHAIN A AND RESID 134:195 )A134 - 195
8X-RAY DIFFRACTION8( CHAIN A AND RESID 196:237 )A196 - 237
9X-RAY DIFFRACTION9( CHAIN A AND RESID 238:275 )A238 - 275

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