[English] 日本語
Yorodumi
- PDB-8afu: DaArgC - N-acetyl-gamma-glutamyl-phosphate Reductase of Denitrovi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8afu
TitleDaArgC - N-acetyl-gamma-glutamyl-phosphate Reductase of Denitrovibrio acetiphilus
ComponentsN-acetyl-gamma-glutamyl-phosphate reductase
KeywordsOXIDOREDUCTASE / Formyl-Phosphate
Function / homology
Function and homology information


N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / arginine biosynthetic process / NADP+ binding / NAD binding / protein dimerization activity / cytoplasm
Similarity search - Function
N-acetyl-gamma-glutamyl-phosphate reductase, type 1 / N-acetyl-gamma-glutamyl-phosphate reductase, active site / N-acetyl-gamma-glutamyl-phosphate reductase active site. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
N-acetyl-gamma-glutamyl-phosphate reductase
Similarity search - Component
Biological speciesDenitrovibrio acetiphilus DSM 12809 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsPfister, P. / Nattermann, M. / Zarzycki, J. / Erb, T.J.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research031B0850B Germany
German Research Foundation (DFG)390919832 Germany
CitationJournal: To Be Published
Title: Engineering a two-enzyme cascade for in vivo formate assimilation.
Authors: Nattermann, M. / Wenk, S. / Pfister, P. / Guntermann, N. / Nickel, L. / Zarzycki, J. / Francio, G. / Leitner, W. / Bar-Even, A. / Erb, T.J.
History
DepositionJul 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-acetyl-gamma-glutamyl-phosphate reductase
B: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4034
Polymers78,3572
Non-polymers462
Water3,963220
1
A: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules

B: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4034
Polymers78,3572
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
2
B: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules

A: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4034
Polymers78,3572
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)86.698, 77.841, 122.026
Angle α, β, γ (deg.)90.000, 92.870, 90.000
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein N-acetyl-gamma-glutamyl-phosphate reductase / AGPR / N-acetyl-glutamate semialdehyde dehydrogenase / NAGSA dehydrogenase


Mass: 39178.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Denitrovibrio acetiphilus DSM 12809 (bacteria)
Strain: DSM 12809 / NBRC 114555 / N2460 / Gene: argC, Dacet_0460 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D4H3H4, N-acetyl-gamma-glutamyl-phosphate reductase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0,2 M Potassium bromide 0,2 M Potassium thiocyanate 0,1 M Sodium cacodylate pH 6.5 3 % w/v gamma-PGA (Na+ form, LM) 2 % v/v PEG 500 MME

-
Data collection

DiffractionMean temperature: 80 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.99→43.294 Å / Num. all: 55251 / Num. obs: 55251 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 34.1 Å2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Rsym value: 0.072 / Net I/av σ(I): 6.3 / Net I/σ(I): 13.4 / Num. measured all: 360748
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.99-2.16.30.5291.44860577500.2250.5760.5293.295.5
2.1-2.236.60.342.25033876750.1430.3690.344.8100
2.23-2.386.30.2263.34542671550.0960.2460.2266.699.6
2.38-2.576.60.1594.54438466930.0660.1730.1599100
2.57-2.816.90.1126.24256261750.0460.1210.11212.3100
2.81-3.156.60.0818.13710555890.0340.0880.0811799.9
3.15-3.636.70.0639.13330049470.0260.0680.06323.899.9
3.63-4.456.50.05211.32705441840.0220.0570.05229.799.8
4.45-6.296.50.04811.82110132660.0210.0520.04831.799.8
6.29-43.29460.04312.71087318170.0190.0470.04331.999.3

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
XDS20220220data reduction
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dr3

3dr3


Resolution: 1.99→43.29 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 1995 3.61 %
Rwork0.1838 53214 -
obs0.185 55209 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.88 Å2 / Biso mean: 45.7611 Å2 / Biso min: 24.93 Å2
Refinement stepCycle: final / Resolution: 1.99→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5217 0 2 220 5439
Biso mean--35.6 49.11 -
Num. residues----673
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.99-2.040.30861130.27583488360191
2.04-2.10.27571600.224837913951100
2.1-2.160.25741320.213738383970100
2.16-2.230.2331530.201138053958100
2.23-2.310.23891440.18893762390699
2.31-2.40.2371410.186838053946100
2.4-2.510.22181350.187438343969100
2.51-2.640.22341500.177937993949100
2.64-2.810.22181420.185138113953100
2.81-3.020.21721390.188438293968100
3.02-3.330.21111420.200538684010100
3.33-3.810.21741500.180238183968100
3.81-4.80.18051420.155938523994100
4.8-43.290.21161520.18213914406699
Refinement TLS params.Method: refined / Origin x: 10.6806 Å / Origin y: -19.2934 Å / Origin z: 50.2905 Å
111213212223313233
T0.2622 Å2-0.0091 Å20.0172 Å2-0.3889 Å2-0.0216 Å2--0.3087 Å2
L0.5847 °2-0.0281 °2-0.0318 °2-0.302 °20.0679 °2--1.2154 °2
S-0.0439 Å °0.0095 Å °0.0111 Å °-0.0235 Å °0.0815 Å °-0.0706 Å °0.0745 Å °0.2321 Å °-0.0326 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-4 - 334
2X-RAY DIFFRACTION1allA351
3X-RAY DIFFRACTION1allB-5 - 334
4X-RAY DIFFRACTION1allB351
5X-RAY DIFFRACTION1allS3 - 223

+
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