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- PDB-8afv: DaArgC3 - Engineered Formyl Phosphate Reductase with 3 substituti... -

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Basic information

Entry
Database: PDB / ID: 8afv
TitleDaArgC3 - Engineered Formyl Phosphate Reductase with 3 substitutions (S178V, G182V, L233I)
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: 2.19 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
C: N-acetyl-gamma-glutamyl-phosphate reductase
D: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,0988
Polymers152,0064
Non-polymers924
Water9,620534
1
A: N-acetyl-gamma-glutamyl-phosphate reductase
B: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0725
Polymers76,0032
Non-polymers693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-44 kcal/mol
Surface area25890 Å2
MethodPISA
2
C: N-acetyl-gamma-glutamyl-phosphate reductase
D: N-acetyl-gamma-glutamyl-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0263
Polymers76,0032
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-24 kcal/mol
Surface area25430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.877, 109.550, 133.225
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 38001.469 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium chloride 0.1 M HEPES pH 7.5 25%(w/v) PEG 4000

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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 PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.19→42.364 Å / Num. obs: 66917 / % possible obs: 97 % / Redundancy: 3.2 % / Biso Wilson estimate: 29.75 Å2 / Rpim(I) all: 0.035 / Rrim(I) all: 0.068 / Rsym value: 0.057 / Net I/av σ(I): 8.8 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.194-2.313.20.1933.697910.1190.2290.19398.3
2.31-2.453.10.141593510.0880.1670.14198.8
2.45-2.623.20.1076.587600.0670.1280.10798.3
2.62-2.833.30.086881090.0520.1010.08697.6
2.83-3.13.20.0679.874530.0410.080.06797.6
3.1-3.473.20.05411.567430.0330.0640.05497.3
3.47-4.013.30.04613.358620.0280.0540.04694.9
4.01-4.913.10.04213.649100.0260.050.04294.4
4.91-6.943.20.04213.838340.0260.050.04294
6.94-42.3642.90.0413.421040.0260.0490.0490.3

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Processing

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

3dr3


Resolution: 2.19→42.36 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 1998 2.99 %
Rwork0.1885 64887 -
obs0.189 66885 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.56 Å2 / Biso mean: 38.5589 Å2 / Biso min: 14.74 Å2
Refinement stepCycle: final / Resolution: 2.19→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10023 0 4 534 10561
Biso mean--32.98 40.84 -
Num. residues----1296
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 (%)
2.19-2.250.25461420.22574621476398
2.25-2.310.22561440.20114676482098
2.31-2.380.22341450.19384670481598
2.38-2.450.23991430.19524668481199
2.45-2.540.22711460.18984716486298
2.54-2.640.21941430.19394636477997
2.64-2.760.25181420.2074617475997
2.76-2.910.23221440.19884670481497
2.91-3.090.21681430.19734638478197
3.09-3.330.19881440.20144662480697
3.33-3.670.22181410.18924620476196
3.67-4.20.17621410.17084534467593
4.2-5.280.16131400.16054572471294
5.29-42.360.20811400.19484587472790
Refinement TLS params.Method: refined / Origin x: -38.4898 Å / Origin y: -1.2472 Å / Origin z: -0.0408 Å
111213212223313233
T0.1544 Å20.0025 Å2-0.0161 Å2-0.2034 Å2-0.0325 Å2--0.175 Å2
L0.4101 °20.098 °20.0253 °2-0.8479 °20.2095 °2--0.447 °2
S-0.0554 Å °0.0872 Å °-0.046 Å °0.0388 Å °0.1166 Å °-0.1154 Å °0.091 Å °0.0703 Å °-0.0232 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 334
2X-RAY DIFFRACTION1allB1 - 334
3X-RAY DIFFRACTION1allC1 - 334
4X-RAY DIFFRACTION1allD1 - 334
5X-RAY DIFFRACTION1allF1 - 4
6X-RAY DIFFRACTION1allS1 - 534

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