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- PDB-5f23: Crystal structure of NH(3)-dependent NAD(+) synthetase Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 5f23
TitleCrystal structure of NH(3)-dependent NAD(+) synthetase Pseudomonas aeruginosa in complex with NAD
ComponentsNH(3)-dependent NAD(+) synthetase
KeywordsLIGASE / NH(3)-dependent NAD(+) synthetase / Pseudomonas / NAD / NAD(+) / synthethase / nadE / 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 / NAD+ biosynthetic process / glutaminase activity / 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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of NH(3)-dependent NAD(+) synthetase Pseudomonas aeruginosa in complex with NAD
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 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_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)31,6213
Polymers30,7631
Non-polymers8592
Water4,810267
1
A: NH(3)-dependent NAD(+) synthetase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)63,2436
Polymers61,5262
Non-polymers1,7174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7130 Å2
ΔGint-37 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.870, 41.190, 64.130
Angle α, β, γ (deg.)90.000, 113.540, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21A-589-

HOH

31A-662-

HOH

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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: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus screen, e1: 10% w/v PEG 20 000, 20% v/v PEG MME 550; 30mM of each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol; 0.1 M MES/imidazole pH 6.5; PsaeA. ...Details: Morpheus screen, e1: 10% w/v PEG 20 000, 20% v/v PEG MME 550; 30mM of each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol; 0.1 M MES/imidazole pH 6.5; PsaeA.00025.a.B1.PW37555 at 23.5 mg/ml; 5 h soak with 5mM NAD; cryo: direct; tray 258195e1, puck hml20-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 20, 2015
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 43281 / Num. obs: 42621 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Biso Wilson estimate: 14.76 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.04 / Χ2: 0.949 / Net I/σ(I): 31.81 / Num. measured all: 432740
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
1.5-1.545.20.9450.3494.4415297320329520.38692.2
1.54-1.580.9370.3325.2617052311829290.36393.9
1.58-1.630.9580.2746.9320973297029120.29498
1.63-1.680.9810.2238.3323360292228720.23898.3
1.68-1.730.990.18110.224025286928370.19298.9
1.73-1.790.9940.14612.3623609271427070.15599.7
1.79-1.860.9960.12214.8924494267926670.12999.6
1.86-1.940.9980.09319.0824522255525510.09899.8
1.94-2.020.9990.07125.3423922240024000.075100
2.02-2.120.9990.05632.9924610237423680.05999.7
2.12-2.240.9990.04939.0223782222722270.052100
2.24-2.370.9990.04344.4523076213621270.04599.6
2.37-2.540.9990.0449.5822225197019620.04299.6
2.54-2.740.9990.03656.4522100188018710.03899.5
2.74-310.03461.9921308170216970.03699.7
3-3.3510.03270.9621146155515500.03399.7
3.35-3.8710.02887.0622289137913770.02999.9
3.87-4.7410.028105.2724452117411710.02999.7
4.74-6.7110.03104.31198469229170.03199.5
6.7110.032104.3106525325270.03399.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_2236)phasing
PHENIX(dev_2236)refinement
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4xfd, apo structure

4xfd


Resolution: 1.5→49.712 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1799 2066 4.85 %Random selection
Rwork0.1384 40548 --
obs0.1404 42614 98.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.18 Å2 / Biso mean: 24.9943 Å2 / Biso min: 10.35 Å2
Refinement stepCycle: final / Resolution: 1.5→49.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 56 271 2309
Biso mean--23.75 33.8 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072181
X-RAY DIFFRACTIONf_angle_d0.8992985
X-RAY DIFFRACTIONf_chiral_restr0.054339
X-RAY DIFFRACTIONf_plane_restr0.006397
X-RAY DIFFRACTIONf_dihedral_angle_d16.5131336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53490.25251300.17062537X-RAY DIFFRACTION92
1.5349-1.57330.2011240.1572553X-RAY DIFFRACTION94
1.5733-1.61590.19821490.14562633X-RAY DIFFRACTION98
1.6159-1.66340.2021290.13682659X-RAY DIFFRACTION98
1.6634-1.71710.211290.13352696X-RAY DIFFRACTION99
1.7171-1.77850.2051430.12982733X-RAY DIFFRACTION100
1.7785-1.84970.19511420.13282702X-RAY DIFFRACTION100
1.8497-1.93390.25671120.13622772X-RAY DIFFRACTION100
1.9339-2.03590.18621460.12132699X-RAY DIFFRACTION100
2.0359-2.16340.16481610.12622713X-RAY DIFFRACTION100
2.1634-2.33040.18291340.12372729X-RAY DIFFRACTION100
2.3304-2.5650.20441470.13932766X-RAY DIFFRACTION100
2.565-2.93610.19111450.14872733X-RAY DIFFRACTION100
2.9361-3.6990.16561270.14252786X-RAY DIFFRACTION100
3.699-500.14531480.14092837X-RAY DIFFRACTION100

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