[English] 日本語
Yorodumi
- PDB-7yqq: Crystal Structure of Xcc NAMPT and its complex with NMN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yqq
TitleCrystal Structure of Xcc NAMPT and its complex with NMN
ComponentsPre-B cell enhancing factor related protein
KeywordsTRANSFERASE / Xcc NAMPT in complexed state with NMN
Function / homology
Function and homology information


nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD+ biosynthetic process
Similarity search - Function
Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinamide phosphoribosyl transferase / Nicotinate/nicotinamide phosphoribosyltransferase / Nicotinate phosphoribosyltransferase (NAPRTase) family / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldolase-type TIM barrel
Similarity search - Domain/homology
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / PHOSPHATE ION / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsXu, G.L. / Ming, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32160064 China
CitationJournal: Commun Biol / Year: 2024
Title: Structural insights into Xanthomonas campestris pv. campestris NAD + biosynthesis via the NAM salvage pathway.
Authors: Xu, G. / Ma, J. / Fang, Q. / Peng, Q. / Jiao, X. / Hu, W. / Zhao, Q. / Kong, Y. / Liu, F. / Shi, X. / Tang, D.J. / Tang, J.L. / Ming, Z.
History
DepositionAug 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pre-B cell enhancing factor related protein
B: Pre-B cell enhancing factor related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8584
Polymers106,4272
Non-polymers4302
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Analytical Ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-39 kcal/mol
Surface area32410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.740, 115.740, 318.110
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-613-

HOH

-
Components

#1: Protein Pre-B cell enhancing factor related protein / Nicotinamide Phosphoribosyltransferase


Mass: 53213.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: 8004 / Gene: XC_0719 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2X5R2
#2: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: ammonium tartrate, N,N-Bis(3-D-gluconamidopropyl) cholamide, N,N-Dimethyldecylamine-N-oxide, NMN

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 12, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.22→106.04 Å / Num. obs: 63152 / % possible obs: 99.9 % / Redundancy: 37.2 % / CC1/2: 0.999 / Net I/σ(I): 21.8
Reflection shellResolution: 2.22→2.28 Å / Num. unique obs: 4525 / CC1/2: 0.775

-
Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YQO

7yqo


Resolution: 2.22→57.87 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2179 1861 3.15 %
Rwork0.1829 57131 -
obs0.184 58992 93.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.66 Å2 / Biso mean: 43.3291 Å2 / Biso min: 20.56 Å2
Refinement stepCycle: final / Resolution: 2.22→57.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7004 0 27 478 7509
Biso mean--67.85 45.66 -
Num. residues----901
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2201-2.28010.36481110.3439333173
2.2801-2.34720.28581240.2488400187
2.3472-2.42290.24311370.2058418091
2.4229-2.50950.2111370.2011423091
2.5095-2.610.23541380.1973427093
2.61-2.72880.27371430.1967434894
2.7288-2.87270.27161470.2008448396
2.8727-3.05260.22411470.1893452597
3.0526-3.28830.22321520.1788456698
3.2883-3.61920.20911480.1682465398
3.6192-4.14280.19921540.1604468199
4.1428-5.21890.16061570.14894796100
5.2189-57.870.21661660.1897506799
Refinement TLS params.Method: refined / Origin x: -17.292 Å / Origin y: -51.9618 Å / Origin z: -4.2112 Å
111213212223313233
T0.201 Å20.0058 Å2-0.0075 Å2-0.299 Å20.0373 Å2--0.4428 Å2
L0.7983 °20.1244 °2-0.1082 °2-0.0928 °20.0222 °2--0.4138 °2
S0.0044 Å °0.0767 Å °0.0573 Å °-0.0165 Å °0.0129 Å °-0.0003 Å °-0.0019 Å °-0.0283 Å °-0.0174 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 468
2X-RAY DIFFRACTION1allA501 - 601
3X-RAY DIFFRACTION1allB1 - 468
4X-RAY DIFFRACTION1allS1 - 478

+
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