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- PDB-8afu: DaArgC - N-acetyl-gamma-glutamyl-phosphate Reductase of Denitrovi... -

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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 / L-arginine biosynthetic process / NADP+ binding / NAD binding / cytoplasm
Similarity search - Function
: / N-acetyl-gamma-glutamyl-phosphate reductase, type 1 / N-acetyl-gamma-glutamyl-phosphate reductase, active site / Semialdehyde dehydrogenase, dimerisation domain / N-acetyl-gamma-glutamyl-phosphate reductase active site. / 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: Nat Commun / Year: 2023
Title: Engineering a new-to-nature cascade for phosphate-dependent formate to formaldehyde conversion in vitro and in vivo.
Authors: Nattermann, M. / Wenk, S. / Pfister, P. / He, H. / Lee, S.H. / Szymanski, W. / Guntermann, N. / Zhu, F. / Nickel, L. / Wallner, C. / Zarzycki, J. / Paczia, N. / Gaissert, N. / Francio, G. / ...Authors: Nattermann, M. / Wenk, S. / Pfister, P. / He, H. / Lee, S.H. / Szymanski, W. / Guntermann, N. / Zhu, F. / Nickel, L. / Wallner, C. / Zarzycki, J. / Paczia, N. / Gaissert, N. / Francio, G. / Leitner, W. / Gonzalez, R. / 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
Revision 1.2Oct 23, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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
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: 2.8 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

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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

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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

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