[English] 日本語
Yorodumi
- PDB-6kg3: Crystal structure of Nicotinic acid mononucleotide adenylyltransf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kg3
TitleCrystal structure of Nicotinic acid mononucleotide adenylyltransferase mutant P22K/Y84V/Y118D/C132Q/W176F from Escherichia coli
ComponentsProbable nicotinate-nucleotide adenylyltransferase
KeywordsTRANSFERASE / Nicotinic acid mononucleotide adenylyltransferase
Function / homology
Function and homology information


NAD salvage / 'de novo' NAD biosynthetic process from aspartate / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding
Similarity search - Function
Nicotinate/nicotinamide nucleotide adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable nicotinate-nucleotide adenylyltransferase / Nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesEscherichia coli NCCP15648 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsXue, S. / Zhao, Z. / Wang, X. / Feng, Y.
CitationJournal: To Be Published
Title: Crystal structure of Nicotinic acid mononucleotide adenylyltransferase mutant P22K/Y84V/Y118D/C132Q/W176F from Escherichia coli
Authors: Xue, S. / Feng, Y. / Zhao, Z. / Wang, X.
History
DepositionJul 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable nicotinate-nucleotide adenylyltransferase
B: Probable nicotinate-nucleotide adenylyltransferase
C: Probable nicotinate-nucleotide adenylyltransferase
D: Probable nicotinate-nucleotide adenylyltransferase
E: Probable nicotinate-nucleotide adenylyltransferase
F: Probable nicotinate-nucleotide adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)146,7596
Polymers146,7596
Non-polymers00
Water00
1
A: Probable nicotinate-nucleotide adenylyltransferase
B: Probable nicotinate-nucleotide adenylyltransferase
D: Probable nicotinate-nucleotide adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)73,3793
Polymers73,3793
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Probable nicotinate-nucleotide adenylyltransferase
E: Probable nicotinate-nucleotide adenylyltransferase
F: Probable nicotinate-nucleotide adenylyltransferase


Theoretical massNumber of molelcules
Total (without water)73,3793
Polymers73,3793
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.912, 129.176, 105.320
Angle α, β, γ (deg.)90.000, 103.177, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Probable nicotinate-nucleotide adenylyltransferase / Deamido-NAD(+) diphosphorylase / Deamido-NAD(+) pyrophosphorylase / Nicotinate mononucleotide ...Deamido-NAD(+) diphosphorylase / Deamido-NAD(+) pyrophosphorylase / Nicotinate mononucleotide adenylyltransferase / NaMN adenylyltransferase


Mass: 24459.758 Da / Num. of mol.: 6 / Mutation: P22K, Y84V, Y118D, C132Q, W176F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli NCCP15648 (bacteria) / Gene: nadD, A610_610 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A222QGJ8, UniProt: P0A752*PLUS, nicotinate-nucleotide adenylyltransferase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 67.76 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 1.4M Sodium phosphate monobasic monohydrate-Potassium phosphate dibasic, pH 8.1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9798 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.08→50 Å / Num. obs: 37906 / % possible obs: 97.48 % / Redundancy: 4.5 % / Biso Wilson estimate: 63.51 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 9.05
Reflection shellResolution: 3.08→3.15 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2771 / % possible all: 69.33

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K4K

1k4k


Resolution: 3.08→45.47 Å / SU ML: 0.4592 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.2449
RfactorNum. reflection% reflection
Rfree0.2676 1855 4.9 %
Rwork0.2409 --
obs0.2422 37872 94.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.05 Å2
Refinement stepCycle: LAST / Resolution: 3.08→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10158 0 0 0 10158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012410416
X-RAY DIFFRACTIONf_angle_d1.466914205
X-RAY DIFFRACTIONf_chiral_restr0.07751578
X-RAY DIFFRACTIONf_plane_restr0.01011884
X-RAY DIFFRACTIONf_dihedral_angle_d3.40526366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.160.3673920.28841911X-RAY DIFFRACTION65.84
3.16-3.260.33741110.29162318X-RAY DIFFRACTION80.03
3.26-3.360.36661290.29942629X-RAY DIFFRACTION89.49
3.36-3.480.35181550.29982869X-RAY DIFFRACTION98.02
3.48-3.620.31431470.28062908X-RAY DIFFRACTION99.61
3.62-3.790.29851540.25132910X-RAY DIFFRACTION99.9
3.79-3.990.26651290.24142922X-RAY DIFFRACTION99.8
3.99-4.240.28361480.2312906X-RAY DIFFRACTION99.74
4.24-4.560.25191510.20782925X-RAY DIFFRACTION99.77
4.56-5.020.23691510.21552907X-RAY DIFFRACTION99.77
5.02-5.750.23561490.21612932X-RAY DIFFRACTION99.77
5.75-7.240.24421640.23852934X-RAY DIFFRACTION99.94
7.24-45.470.21861750.22662946X-RAY DIFFRACTION99.05

+
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://pdbjlvh1.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