[English] 日本語
Yorodumi
- PDB-5wp0: Crystal structure of NAD synthetase NadE from Vibrio fischeri -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more