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- PDB-3hmq: 1.9 Angstrom resolution crystal structure of a NAD synthetase (na... -

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Basic information

Entry
Database: PDB / ID: 3hmq
Title1.9 Angstrom resolution crystal structure of a NAD synthetase (nadE) from Salmonella typhimurium LT2 in complex with NAD(+)
ComponentsNH(3)-dependent NAD(+) synthetase
KeywordsLIGASE / NAD Synthetase (nadE) / Structural Genomics / Infectious Diseases / Center for Structural Genomics of Infectious Diseases / ATP-binding / NAD / Nucleotide-binding / CSGID
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NH(3)-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHalavaty, A.S. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.9 Angstrom resolution crystal structure of a NAD synthetase (nadE) from Salmonella typhimurium LT2 in complex with NAD(+)
Authors: Halavaty, A.S. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 7, 2011Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,14210
Polymers30,7101
Non-polymers1,4329
Water7,782432
1
A: NH(3)-dependent NAD(+) synthetase
hetero molecules

A: NH(3)-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,28420
Polymers61,4202
Non-polymers2,86418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area10260 Å2
ΔGint-253 kcal/mol
Surface area22500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.820, 91.820, 75.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 30710.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: nadE, STM1310 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: Q8ZPU5, NAD+ synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: protein in 300mM NaCl, 10mM Hepes Na pH 7.5, 0.5mM TCEP was mixed at 1:1 v/v ratio with NH4Sulphat 2M, Bis-Tris 0.1m pH 5.5, 10mm NAD-magic solution, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2009 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→29.06 Å / Num. all: 29311 / Num. obs: 29311 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Biso Wilson estimate: 29.9 Å2 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1350 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
REFMAC5.5.0051refinement
XSCALEdata scaling
XDSdata reduction
XDSdata scaling
StructureSolution Crank (SHELXCphasing
SHELXDphasing
SHELXEmodel building
Bp3phasing
SOLOMONphasing
ARPin CCP4model building
WARPin CCP4model building
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.06 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.607 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1866 1477 5.1 %RANDOM
Rwork0.14404 ---
obs0.14611 27647 99.74 %-
all-27647 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.529 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å20 Å2
2---0.4 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 84 432 2565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222325
X-RAY DIFFRACTIONr_bond_other_d0.0010.021573
X-RAY DIFFRACTIONr_angle_refined_deg1.3742.0043169
X-RAY DIFFRACTIONr_angle_other_deg0.91833844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3365289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.61124.364110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.83815406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1941517
X-RAY DIFFRACTIONr_chiral_restr0.0910.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022608
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02465
X-RAY DIFFRACTIONr_mcbond_it0.6981.51386
X-RAY DIFFRACTIONr_mcbond_other0.1961.5565
X-RAY DIFFRACTIONr_mcangle_it1.2222237
X-RAY DIFFRACTIONr_scbond_it1.9113939
X-RAY DIFFRACTIONr_scangle_it3.0564.5932
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 98 -
Rwork0.174 2044 -
obs-2044 100 %
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)
11.23250.27490.18361.0209-0.11280.6046-0.06690.10120.1142-0.09220.05780.0117-0.08670.01020.00910.0333-0.0158-0.00550.01560.01050.0114-16.728253.0826-2.5387
21.21960.2363-0.87850.6495-1.59013.9856-0.15460.2417-0.365-0.3138-0.0069-0.02130.76310.01580.16150.1952-0.03640.03930.1391-0.05840.1523-12.598928.2114-3.6946
30.65050.3327-0.21070.7793-0.26210.59-0.06940.0881-0.0652-0.1420.0416-0.02780.0868-0.01070.02780.0309-0.01020.00680.0163-0.00880.0067-19.788737.0251.0158
48.71992.797-2.32440.9875-0.70790.6371-0.2710.4064-0.0989-0.1680.22970.03240.0477-0.05560.04120.2121-0.0668-0.04720.19350.01340.1266-28.580237.0241-14.9581
50.56850.2170.06470.48470.03982.2913-0.04530.04290.1164-0.09020.05970.2086-0.0618-0.2457-0.01440.0188-0.0067-0.03860.03850.0310.0916-39.753644.9842.6192
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 80
2X-RAY DIFFRACTION2A81 - 91
3X-RAY DIFFRACTION3A92 - 202
4X-RAY DIFFRACTION4A203 - 228
5X-RAY DIFFRACTION5A229 - 275

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