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- PDB-5wp0: Crystal structure of NAD synthetase NadE from Vibrio fischeri -

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Basic information

Entry
Database: PDB / ID: 5wp0
TitleCrystal structure of NAD synthetase NadE from Vibrio fischeri
ComponentsNH(3)-dependent NAD(+) synthetase
KeywordsLIGASE / Structural genomics / NIAID / National Institute of Allergy and Infectious Diseases / ALPHA BETA / 3-LAYER(ABA) SANDWICH / ROSSMANN FOLD / NAD SYNTHETASE / Center for Structural Genomics of Infectious Diseases / CSGID
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
NH(3)-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsStogios, P.J. / Evdokimova, E. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionAug 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jun 18, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _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: NH(3)-dependent NAD(+) synthetase
B: NH(3)-dependent NAD(+) synthetase


Theoretical massNumber of molelcules
Total (without water)61,4402
Polymers61,4402
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-45 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.252, 115.887, 55.086
Angle α, β, γ (deg.)90.00, 112.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30719.889 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (strain ATCC 700601 / ES114) (bacteria)
Strain: ATCC 700601 / ES114 / Gene: nadE, VF_A0602 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Gold Magic / References: UniProt: Q5DZX4, NAD+ synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M MgCl2, 0.1 M HEPES pH 7.5, 21% PEG 3350, 0.5 mM CaCl2

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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 RAXIS HTC / Detector: IMAGE PLATE / Date: May 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 17622 / % possible obs: 99.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.087 / Net I/σ(I): 9.33
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 878 / CC1/2: 0.717 / Rpim(I) all: 0.398 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIXdev_2733refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3q4g

3q4g


Resolution: 2.6→24.867 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.95
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 864 4.97 %RANDOM
Rwork0.2003 ---
obs0.2034 17373 97.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→24.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4129 0 0 191 4320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024188
X-RAY DIFFRACTIONf_angle_d0.4535649
X-RAY DIFFRACTIONf_dihedral_angle_d22.0181582
X-RAY DIFFRACTIONf_chiral_restr0.038645
X-RAY DIFFRACTIONf_plane_restr0.003741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5914-2.75360.3331360.2832508X-RAY DIFFRACTION89
2.7536-2.96590.36691440.26442763X-RAY DIFFRACTION99
2.9659-3.26380.32691460.24552805X-RAY DIFFRACTION100
3.2638-3.73470.29611430.20322796X-RAY DIFFRACTION100
3.7347-4.70010.21531400.16382804X-RAY DIFFRACTION100
4.7001-24.86830.2021550.16842833X-RAY DIFFRACTION99
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)
15.98950.62783.55372.25541.56222.7875-0.74660.171.1607-1.5305-0.5301-0.24570.24510.20741.18230.680.03830.13280.5439-0.01270.912717.9544.5222-19.9888
24.3374-0.75030.66282.37570.26112.390.12860.26720.1088-0.3271-0.05060.1497-0.2857-0.2425-0.08840.37210.04490.02020.2707-0.00650.344-12.7670.8988-22.4133
36.1234-5.60814.49797.2172-6.41185.8674-0.3358-0.56730.50631.1210.11160.2006-0.5622-0.07720.17560.4571-0.01230.0120.5214-0.06940.3752-13.7173-8.6096-2.1393
48.21677.65560.31317.2028-0.44548.05490.7679-1.71540.40492.988-0.2356-0.89961.1808-0.148-0.59211.4443-0.0281-0.05031.0919-0.26010.66352.4204-12.58958.4439
50.4848-0.2788-0.11462.8978-0.09350.85460.1719-0.12210.25140.2905-0.0286-0.273-0.19630.0356-0.13340.3354-0.010.00850.324-0.05010.355-0.1088-1.1359-13.5215
62.314-0.23830.02191.30690.31560.47820.0213-0.1551-0.016-0.0316-0.0026-0.10680.08490.0582-0.02190.3073-0.00060.00090.28520.05760.29379.8801-28.9237-15.5889
74.78422.5324-1.73331.342-0.91850.6281-0.70630.5768-1.7307-1.7488-0.91180.0327-0.5664-0.09891.07391.372-0.05660.33371.5015-0.41430.6861-10.6907-38.6882-5.6086
86.9471-3.8114-0.03144.7604-0.75052.7406-0.1676-0.2844-0.37060.31710.15480.50.0662-0.2469-0.01140.303-0.08990.07620.30770.01240.3332-11.1154-26.0284-5.3156
91.01181.7881-1.85418.13961.3819.2723-0.46070.35380.607-0.15590.5817-0.21290.69110.0684-0.16840.2443-0.0205-0.1040.44750.15020.6207-25.5602-22.1421-17.0087
100.6913-0.299-0.70871.50610.72120.88120.07120.0810.0145-0.003-0.05320.0894-0.0401-0.1903-0.00990.30670.004-0.02520.3210.0390.3219-2.761-27.9174-22.9369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -2:3 )A-2 - 3
2X-RAY DIFFRACTION2( CHAIN A AND RESID 4:85 )A4 - 85
3X-RAY DIFFRACTION3( CHAIN A AND RESID 86:129 )A86 - 129
4X-RAY DIFFRACTION4( CHAIN A AND RESID 130:137 )A130 - 137
5X-RAY DIFFRACTION5( CHAIN A AND RESID 138:276 )A138 - 276
6X-RAY DIFFRACTION6( CHAIN B AND RESID -2:82 )B-2 - 82
7X-RAY DIFFRACTION7( CHAIN B AND RESID 83:89 )B83 - 89
8X-RAY DIFFRACTION8( CHAIN B AND RESID 90:128 )B90 - 128
9X-RAY DIFFRACTION9( CHAIN B AND RESID 129:138 )B129 - 138
10X-RAY DIFFRACTION10( CHAIN B AND RESID 139:276 )B139 - 276

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