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- PDB-6kv3: Crystal Structure of NAD+ Synthetase from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 6kv3
TitleCrystal Structure of NAD+ Synthetase from Staphylococcus aureus
ComponentsNH(3)-dependent NAD(+) synthetase
KeywordsLIGASE / Staphylococcus aureus / NAD synthetase Nucleotide-binding protein / NAD pathway
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 / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
NH(3)-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNasrin, S.K. / Sandeep, S.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India)BT/BI/12/045/2008 India
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Crystallographic and molecular dynamics simulation analysis of NAD synthetase from methicillin resistant Staphylococcus aureus (MRSA).
Authors: Sultana, K.N. / Kuldeep, J. / Siddiqi, M.I. / Srivastava, S.K.
History
DepositionSep 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: NH(3)-dependent NAD(+) synthetase
C: NH(3)-dependent NAD(+) synthetase
B: NH(3)-dependent NAD(+) synthetase
D: NH(3)-dependent NAD(+) synthetase


Theoretical massNumber of molelcules
Total (without water)127,2284
Polymers127,2284
Non-polymers00
Water12,881715
1
A: NH(3)-dependent NAD(+) synthetase
B: NH(3)-dependent NAD(+) synthetase


Theoretical massNumber of molelcules
Total (without water)63,6142
Polymers63,6142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-30 kcal/mol
Surface area21840 Å2
MethodPISA
2
C: NH(3)-dependent NAD(+) synthetase
D: NH(3)-dependent NAD(+) synthetase


Theoretical massNumber of molelcules
Total (without water)63,6142
Polymers63,6142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-28 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.979, 107.714, 93.986
Angle α, β, γ (deg.)90.000, 96.720, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 86 or resid 89...
21(chain B and (resid 3 through 86 or resid 89...
31(chain C and (resid 3 through 86 or resid 89...
41(chain D and resid 3 through 270)

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
11LYSLYSVALVAL(chain A and (resid 3 through 86 or resid 89...AA3 - 863 - 86
12ASPASPILEILE(chain A and (resid 3 through 86 or resid 89...AA89 - 16689 - 166
13TYRTYRGLUGLU(chain A and (resid 3 through 86 or resid 89...AA170 - 203170 - 203
14GLYGLYTRPTRP(chain A and (resid 3 through 86 or resid 89...AA227 - 270227 - 270
21LYSLYSVALVAL(chain B and (resid 3 through 86 or resid 89...BC3 - 863 - 86
22ASPASPILEILE(chain B and (resid 3 through 86 or resid 89...BC89 - 16689 - 166
23TYRTYRGLUGLU(chain B and (resid 3 through 86 or resid 89...BC170 - 203170 - 203
24GLYGLYTRPTRP(chain B and (resid 3 through 86 or resid 89...BC227 - 270227 - 270
31LYSLYSVALVAL(chain C and (resid 3 through 86 or resid 89...CB3 - 863 - 86
32ASPASPILEILE(chain C and (resid 3 through 86 or resid 89...CB89 - 16689 - 166
33TYRTYRGLUGLU(chain C and (resid 3 through 86 or resid 89...CB170 - 203170 - 203
34GLYGLYTRPTRP(chain C and (resid 3 through 86 or resid 89...CB227 - 270227 - 270
41LYSLYSTRPTRP(chain D and resid 3 through 270)DD3 - 2703 - 270

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Components

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


Mass: 31806.959 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs.
Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria)
Strain: COL / Gene: nadE, SACOL1974 / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5HEK9, NAD+ synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Description: Rod shaped morphology Dimension 0.4 X 0.1 X 0.1 mm
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 200 mM Calcium chloride, 100mM Tris-HCl pH7.5, 22% PEG 4000,
PH range: 7.2-8.0 / Temp details: Temperature was maintained at incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryo system / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 9, 2012 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.3→70.54 Å / Num. obs: 44717 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 17.197 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.033 / Rrim(I) all: 0.065 / Χ2: 1.03 / Net I/σ(I): 20
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 12.3 / Num. unique obs: 4382 / CC1/2: 0.991 / Rpim(I) all: 0.052 / Rrim(I) all: 0.106 / Χ2: 0.94 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NSY

1nsy


Resolution: 2.3→46.671 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.49
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 3896 4.46 %Anomalous flag
Rwork0.211 ---
obs0.2135 44556 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.99 Å2 / Biso mean: 28.2412 Å2 / Biso min: 3.2 Å2
Refinement stepCycle: final / Resolution: 2.3→46.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7771 0 0 715 8486
Biso mean---29.86 -
Num. residues----992
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2876X-RAY DIFFRACTION11.742TORSIONAL
12B2876X-RAY DIFFRACTION11.742TORSIONAL
13C2876X-RAY DIFFRACTION11.742TORSIONAL
14D2876X-RAY DIFFRACTION11.742TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.32810.29271430.20253025100
2.3281-2.35750.22871410.19062987100
2.3575-2.38850.29361410.20153032100
2.3885-2.42130.28671440.21143045100
2.4213-2.45580.3021400.20162943100
2.4558-2.49250.30321410.20293006100
2.4925-2.53140.30621420.21183030100
2.5314-2.57290.26041380.20562954100
2.5729-2.61730.29331420.22223018100
2.6173-2.66490.31531400.2184299699
2.6649-2.71620.28011340.2183293198
2.7162-2.77160.26651410.20133011100
2.7716-2.83180.25251440.2063077100
2.8318-2.89770.27491400.20582919100
2.8977-2.97020.27481390.21693065100
2.9702-3.05050.27341390.20672970100
3.0505-3.14020.28821430.20363023100
3.1402-3.24150.2621410.20083005100
3.2415-3.35740.2411360.20233010100
3.3574-3.49170.32011360.2567295999
3.4917-3.65060.3061360.2901291797
3.6506-3.8430.35011290.2876272390
3.843-4.08360.31721370.2488295098
4.0836-4.39870.1831380.16022985100
4.3987-4.84090.1871410.15063034100
4.8409-5.54050.2261390.16243020100
5.5405-6.97670.22841390.19232997100
6.9767-46.6710.16941320.1465281993
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)
10.7511-0.2972-0.32130.3958-0.10120.97680.0477-0.02870.0443-0.01510.01180.10310.07040.0916-0.04310.1747-0.0077-0.00260.2099-0.030.22490.53471.58776.9104
20.48760.031-0.00231.5320.4650.7417-0.04080.04230.1168-0.02260.0866-0.1631-0.08380.0946-0.02350.16840.00140.01460.19570.01930.2137-36.355621.733969.95
30.50040.22350.22181.31340.59340.2772-0.13350.0930.01410.050.12830.02110.02320.04420.01320.1813-0.003-0.00780.2436-0.00160.2119-3.126324.918819.8242
40.68370.2686-0.24930.4907-0.12460.85940.10610.1474-0.0284-0.1267-0.0384-0.00120.13050.1184-0.05520.19570.0246-0.01350.2479-0.03260.1767-29.8862.071953.2984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 2:270)A2 - 270
2X-RAY DIFFRACTION2(chain C and resseq 2:270)C2 - 270
3X-RAY DIFFRACTION3(chain B and resseq 2:271)B2 - 271
4X-RAY DIFFRACTION4(chain D and resseq 3:273)D3 - 273

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