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- PDB-5kha: Structure of glutamine-dependent NAD+ synthetase from Acinetobact... -

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Basic information

Entry
Database: PDB / ID: 5kha
TitleStructure of glutamine-dependent NAD+ synthetase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP)
ComponentsGlutamine-dependent NAD+ synthetase
KeywordsLIGASE / SSGCID / Acinetobacter baumannii / Glutamine-dependent NAD+ synthetase / nadE / ADP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


NAD+ synthase (glutamine-hydrolysing) / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Glutamine-dependent NAD(+) synthetase / NAD(+) synthetase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / NAD/GMP synthase / NAD synthase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase ...Glutamine-dependent NAD(+) synthetase / NAD(+) synthetase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / NAD/GMP synthase / NAD synthase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Glutamine-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of glutamine-dependent NAD+ synthetase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP)
Authors: Abendroth, J. / Delker, S.L. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJun 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Structure summary
Revision 1.2Sep 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_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamine-dependent NAD+ synthetase
B: Glutamine-dependent NAD+ synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,0598
Polymers123,0092
Non-polymers1,0496
Water11,205622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-87 kcal/mol
Surface area36890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.880, 123.750, 73.650
Angle α, β, γ (deg.)90.000, 110.930, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2:30 or resid 32:33 or (resid...
21(chain B and (resid 2:22 or (resid 23 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSASNASN(chain A and (resid 2:30 or resid 32:33 or (resid...AA2 - 3010 - 38
12ALAALALYSLYS(chain A and (resid 2:30 or resid 32:33 or (resid...AA32 - 3340 - 41
13LYSLYSLYSLYS(chain A and (resid 2:30 or resid 32:33 or (resid...AA3442
14LYSLYSCLCL(chain A and (resid 2:30 or resid 32:33 or (resid...AA - E2 - 60210
15LYSLYSCLCL(chain A and (resid 2:30 or resid 32:33 or (resid...AA - E2 - 60210
16LYSLYSCLCL(chain A and (resid 2:30 or resid 32:33 or (resid...AA - E2 - 60210
17LYSLYSCLCL(chain A and (resid 2:30 or resid 32:33 or (resid...AA - E2 - 60210
21LYSLYSTHRTHR(chain B and (resid 2:22 or (resid 23 and (name...BB2 - 2210 - 30
22GLNGLNGLNGLN(chain B and (resid 2:22 or (resid 23 and (name...BB2331
23METMETCLCL(chain B and (resid 2:22 or (resid 23 and (name...BB - H1 - 6029
24METMETCLCL(chain B and (resid 2:22 or (resid 23 and (name...BB - H1 - 6029
25METMETCLCL(chain B and (resid 2:22 or (resid 23 and (name...BB - H1 - 6029
26METMETCLCL(chain B and (resid 2:22 or (resid 23 and (name...BB - H1 - 6029

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Components

#1: Protein Glutamine-dependent NAD+ synthetase / NAD synthetase / NAD synthetase / Glutamine amidotransferase chain of NAD synthetase / NAD ...NAD synthetase / NAD synthetase / Glutamine amidotransferase chain of NAD synthetase / NAD synthetase/glutamine amidotransferase chain of NAD synthetase / NAD+ synthase / NAD+ synthetase


Mass: 61504.609 Da / Num. of mol.: 2 / Fragment: AcbaC.18002.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: nadE, A7A43_14755, AB895_2341, AB988_2173, ABUW_3069, ACX60_14085, APD31_16600, AQ480_16865, IOMTU433_2979, IX87_01870, TE32_15345
Plasmid: AcbaC.18002.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: V5VHL3, NAD+ synthase (glutamine-hydrolysing), NAD+ synthase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.49 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG1, condition H5: 20% PEG 3350, 200mM KCl; AcbaC.18002.a.B1.PS02475 at 19.5mg/ml with 2mM of each AMPPNP, Glutamate, MgCl2, PPi; cryo: 20% EG with 2mM NAD/Mg; puck: exo0-1, tray: 266048 h5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 25, 2016 / Details: Rigaku Varimax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 69741 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 24.12 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.099 / Net I/σ(I): 10.83
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.150.542.58198
2.15-2.210.4783.35199.4
2.21-2.280.4293.67198.8
2.28-2.350.3934199.4
2.35-2.420.3284.56199.4
2.42-2.510.3014.76199.7
2.51-2.60.2445.73199.7
2.6-2.710.2186.21199.7
2.71-2.830.1737.14199.6
2.83-2.970.1517.6199.7
2.97-3.130.1169.29199.8
3.13-3.320.08712.421100
3.32-3.550.06418.12199.8
3.55-3.830.05423.7199.5
3.83-4.20.04527.18199
4.2-4.70.03930.9198.9
4.7-5.420.03927.98199.6
5.42-6.640.04622.08199.4
6.64-9.390.03229.89199.5
9.39-500.02344.1195.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.1 Å41.24 Å
Translation2.1 Å41.24 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
PHENIXmodel building
PHENIXdev_2429refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4f4h

4f4h


Resolution: 2.1→41.242 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.72
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 2060 2.96 %RANDOM
Rwork0.165 ---
obs0.1663 69703 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.3 Å2 / Biso mean: 33.9518 Å2 / Biso min: 9.8 Å2
Refinement stepCycle: final / Resolution: 2.1→41.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8096 0 64 627 8787
Biso mean--33.5 38.05 -
Num. residues----1052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078393
X-RAY DIFFRACTIONf_angle_d0.89811414
X-RAY DIFFRACTIONf_chiral_restr0.0551298
X-RAY DIFFRACTIONf_plane_restr0.0051511
X-RAY DIFFRACTIONf_dihedral_angle_d15.2845044
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4741X-RAY DIFFRACTION7.767TORSIONAL
12B4741X-RAY DIFFRACTION7.767TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14890.31741410.24874399454098
2.1489-2.20260.23321660.215844704636100
2.2026-2.26220.25871340.24483461799
2.2622-2.32870.26111180.19774520463899
2.3287-2.40390.25791470.185444714618100
2.4039-2.48980.27911140.187945324646100
2.4898-2.58950.27041390.17944914630100
2.5895-2.70730.24441340.171845284662100
2.7073-2.850.19721330.169945204653100
2.85-3.02850.23581220.172845414663100
3.0285-3.26220.22171820.166345134695100
3.2622-3.59040.18721290.146545424671100
3.5904-4.10950.14421060.14144550465699
4.1095-5.17590.17141460.12674513465999
5.1759-41.24950.18851490.16464570471999
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)
12.59160.1027-0.20810.89790.11971.1950.09370.00340.2637-0.00830.0672-0.2416-0.28640.3312-0.1290.2133-0.07850.02830.2455-0.05950.26131.44535.940656.5893
22.35550.1981-1.13640.96520.00482.0526-0.07430.069-0.3246-0.09480.0789-0.16450.13890.2685-0.00350.151-0.0011-0.02590.1929-0.04990.2293-1.3372-10.539258.661
31.5285-0.8346-0.56720.80220.58471.0233-0.0923-0.3639-0.18760.20450.07560.11530.09680.02610.01310.3269-0.03910.03630.24650.0190.1921-27.3234-3.911588.0476
41.4555-1.13710.531.26-0.53841.64290.0944-0.1432-0.43940.34280.04550.22520.4620.113-0.10790.3299-0.01120.06320.21950.05230.2538-17.9913-14.733283.0363
51.5421.9162-0.36697.3107-0.58251.2299-0.12680.0085-0.04880.01960.0933-0.43410.11670.03390.05070.24830.0115-0.01460.149-0.03240.2634-17.53224.804471.1054
62.8539-1.78330.60511.1278-0.22771.9947-0.03240.02120.13370.05670.0328-0.1195-0.03410.1170.00110.2976-0.00590.02560.1512-0.02550.267-20.271615.588165.163
71.79820.0630.39851.33580.53732.17510.05350.3552-0.199-0.2465-0.1860.2067-0.0234-0.49070.02560.20590.0432-0.02850.3782-0.07180.2153-38.97235.562441.3729
81.4207-0.10530.14291.25380.94551.590.1160.38730.2087-0.4371-0.1450.0391-0.6146-0.29020.04920.39710.134-0.00860.30450.04520.2086-38.587921.864444.7664
91.3501-0.3203-0.07951.241-0.32332.29860.0531-0.29060.26990.4129-0.01580.1146-0.4973-0.2632-0.04620.3350.02660.04390.296-0.06290.2476-46.243619.969481.4772
100.6557-0.2421-0.22411.2784-1.2971.5711-0.0633-0.28070.11090.256-0.0606-0.0677-0.21070.030.14260.3173-0.02970.03370.2384-0.04750.1923-32.500812.401785.1561
111.6494-0.7725-0.20110.925-0.59681.18820.1296-0.11920.52060.3554-0.03920.3517-0.4889-0.2365-0.00630.34590.04470.05060.2338-0.05290.2803-42.084426.707273.778
120.94490.62490.05184.76150.2691.552-0.0210.01390.0302-0.16970.12220.4876-0.026-0.0886-0.04660.1971-0.0239-0.02380.14070.010.2712-34.7458-12.97164.8507
130.0669-0.0001-0.29982.91040.01391.3284-0.005-0.01940.2025-0.04850.04850.181-0.0449-0.2778-0.01860.1797-0.0082-0.01770.2110.0130.2189-28.4161-3.947662.0862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 139 )A2 - 139
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 277 )A140 - 277
3X-RAY DIFFRACTION3chain 'A' and (resid 278 through 421 )A278 - 421
4X-RAY DIFFRACTION4chain 'A' and (resid 422 through 466 )A422 - 466
5X-RAY DIFFRACTION5chain 'A' and (resid 467 through 513 )A467 - 513
6X-RAY DIFFRACTION6chain 'A' and (resid 514 through 541 )A514 - 541
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 139 )B1 - 139
8X-RAY DIFFRACTION8chain 'B' and (resid 140 through 277 )B140 - 277
9X-RAY DIFFRACTION9chain 'B' and (resid 278 through 343 )B278 - 343
10X-RAY DIFFRACTION10chain 'B' and (resid 344 through 421 )B344 - 421
11X-RAY DIFFRACTION11chain 'B' and (resid 422 through 466 )B422 - 466
12X-RAY DIFFRACTION12chain 'B' and (resid 467 through 513 )B467 - 513
13X-RAY DIFFRACTION13chain 'B' and (resid 514 through 541 )B514 - 541

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