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- PDB-9w5w: Crystal structure of Namat in complex with NAD -

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Basic information

Entry
Database: PDB / ID: 9w5w
TitleCrystal structure of Namat in complex with NAD
ComponentsNicotinamide phosphoribosyltransferase
KeywordsVIRAL PROTEIN / Namat / NAD / Phage / bacterial immunity / immune evasion
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / :
Function and homology information
Biological speciesBacillus phage SPbetaL1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBao, H. / Xu, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: Structural evolution of the selectivity clamp confers ADPR-PP specificity in Namat, a phage nicotinamide ADP-ribose transferase.
Authors: Lan, M. / Xu, L. / Han, Y. / Cui, T. / Qiao, Z. / Teng, Y.B. / Wang, N. / Bao, H.
History
DepositionAug 2, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nicotinamide phosphoribosyltransferase
B: Nicotinamide phosphoribosyltransferase
C: Nicotinamide phosphoribosyltransferase
D: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,97613
Polymers224,8464
Non-polymers3,1309
Water17,366964
1
A: Nicotinamide phosphoribosyltransferase
B: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0347
Polymers112,4232
Non-polymers1,6115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-83 kcal/mol
Surface area33560 Å2
MethodPISA
2
C: Nicotinamide phosphoribosyltransferase
D: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9426
Polymers112,4232
Non-polymers1,5194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11630 Å2
ΔGint-87 kcal/mol
Surface area33860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.039, 104.525, 119.763
Angle α, β, γ (deg.)109.25, 100.66, 90.36
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nicotinamide phosphoribosyltransferase


Mass: 56211.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage SPbetaL1 (virus) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A9Y1YVZ0, nicotinamide phosphoribosyltransferase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 964 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium chloride, 0.1 M HEPES pH 7.5, 1.6 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.3→49.21 Å / Num. obs: 115304 / % possible obs: 90.3 % / Redundancy: 2.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.078 / Rrim(I) all: 0.135 / Χ2: 0.81 / Net I/σ(I): 6.7 / Num. measured all: 301867
Reflection shellResolution: 2.3→2.34 Å / % possible obs: 93.5 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.402 / Num. measured all: 15650 / Num. unique obs: 5897 / CC1/2: 0.753 / Rpim(I) all: 0.287 / Rrim(I) all: 0.496 / Χ2: 0.9 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
autoPXdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.21 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2289 5612 4.88 %
Rwork0.1853 --
obs0.1874 114969 90.03 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15459 0 202 964 16625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416016
X-RAY DIFFRACTIONf_angle_d0.7421744
X-RAY DIFFRACTIONf_dihedral_angle_d8.132110
X-RAY DIFFRACTIONf_chiral_restr0.0492433
X-RAY DIFFRACTIONf_plane_restr0.0062753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.28881860.22333780X-RAY DIFFRACTION94
2.33-2.350.25742240.21863792X-RAY DIFFRACTION93
2.35-2.380.26171950.21733730X-RAY DIFFRACTION93
2.38-2.410.27971940.21613725X-RAY DIFFRACTION92
2.41-2.440.23941870.2133771X-RAY DIFFRACTION92
2.44-2.480.27982010.22033614X-RAY DIFFRACTION90
2.48-2.510.30411920.22463478X-RAY DIFFRACTION87
2.51-2.550.28512180.22033898X-RAY DIFFRACTION94
2.55-2.590.25231820.20953738X-RAY DIFFRACTION94
2.59-2.630.25762040.20723784X-RAY DIFFRACTION94
2.63-2.680.27051130.20562309X-RAY DIFFRACTION56
2.68-2.730.24981860.20363757X-RAY DIFFRACTION94
2.73-2.780.26431680.20093830X-RAY DIFFRACTION93
2.78-2.840.23631920.19453732X-RAY DIFFRACTION93
2.84-2.90.25011910.19393736X-RAY DIFFRACTION92
2.9-2.970.24372150.20463646X-RAY DIFFRACTION91
2.97-3.040.27381870.2043595X-RAY DIFFRACTION88
3.04-3.120.2521800.20663477X-RAY DIFFRACTION87
3.12-3.210.24632010.19343882X-RAY DIFFRACTION95
3.21-3.320.23721810.18523803X-RAY DIFFRACTION94
3.32-3.440.2342160.18193738X-RAY DIFFRACTION93
3.44-3.570.22471730.17753776X-RAY DIFFRACTION92
3.57-3.740.21612110.16863649X-RAY DIFFRACTION90
3.74-3.930.19471700.16693510X-RAY DIFFRACTION87
3.93-4.180.17211630.15253543X-RAY DIFFRACTION87
4.18-4.50.17731930.14163778X-RAY DIFFRACTION93
4.5-4.950.1691690.14543740X-RAY DIFFRACTION92
4.95-5.670.19931600.17383522X-RAY DIFFRACTION87
5.67-7.140.22691830.19183494X-RAY DIFFRACTION86
7.14-49.210.1951770.18013530X-RAY DIFFRACTION87
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)
11.09260.66310.26381.69790.34650.98830.0298-0.03630.07550.1425-0.04750.267-0.1929-0.1810.0180.16530.05890.03520.2190.01290.1318-9.6619-0.04586.698
20.6660.0625-0.09322.3937-0.53181.04560.01540.07910.0037-0.02420.0051-0.0207-0.1477-0.0109-0.02110.08160.008-0.01050.1649-0.00590.10057.93450.1381-8.1968
31.3356-0.67310.16091.6347-0.16551.12840.04520.02810.1362-0.1523-0.0331-0.2282-0.26950.1978-0.01130.1996-0.0720.03550.198-0.01540.133716.940712.772246.7047
40.6134-0.0463-0.03692.43670.70171.102-0.002-0.07030.0525-0.05340.00810.0487-0.1724-0.0214-0.00620.0840.0076-0.01490.16780.00590.1136-0.573212.754861.3699
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 491)
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 491)
3X-RAY DIFFRACTION3(chain 'C' and resid 3 through 491)
4X-RAY DIFFRACTION4(chain 'D' and resid -4 through 491)

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