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- PDB-7p41: Crystal Structure of human mARC1 A165T Variant -

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Basic information

Entry
Database: PDB / ID: 7p41
TitleCrystal Structure of human mARC1 A165T Variant
ComponentsMitochondrial amidoxime-reducing component 1,Endolysin,Mitochondrial amidoxime-reducing component 1
KeywordsMETAL BINDING PROTEIN / molybdenum Cofactor / molybdenum enzyme / molybdopterin / pyranopterin / mARC
Function / homology
Function and homology information


nitrate metabolic process / detoxification of nitrogen compound / nitric-oxide synthase complex / cellular detoxification of nitrogen compound / nitrate reductase activity / oxidoreductase activity, acting on other nitrogenous compounds as donors / molybdenum ion binding / Phase I - Functionalization of compounds / molybdopterin cofactor binding / Oxidoreductases; Acting on other nitrogenous compounds as donors ...nitrate metabolic process / detoxification of nitrogen compound / nitric-oxide synthase complex / cellular detoxification of nitrogen compound / nitrate reductase activity / oxidoreductase activity, acting on other nitrogenous compounds as donors / molybdenum ion binding / Phase I - Functionalization of compounds / molybdopterin cofactor binding / Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / viral release from host cell by cytolysis / nitric oxide biosynthetic process / peptidoglycan catabolic process / cell wall macromolecule catabolic process / pyridoxal phosphate binding / lysozyme / lysozyme activity / host cell cytoplasm / mitochondrial outer membrane / defense response to bacterium / mitochondrion
Similarity search - Function
MOSC, N-terminal beta barrel / MOSC N-terminal beta barrel domain / Molybdenum cofactor sulfurase, C-terminal / MOSC domain / MOSC domain profile. / Pyruvate kinase-like, insert domain superfamily / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 ...MOSC, N-terminal beta barrel / MOSC N-terminal beta barrel domain / Molybdenum cofactor sulfurase, C-terminal / MOSC domain / MOSC domain profile. / Pyruvate kinase-like, insert domain superfamily / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
oxidanyl(oxidanylidene)molybdenum / Chem-MTE / Endolysin / Mitochondrial amidoxime-reducing component 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsStruwe, M.A. / Scheidig, A.J.
CitationJournal: Hepatol Commun / Year: 2022
Title: Letter to the editor: The clinically relevant MTARC1 p.Ala165Thr variant impacts neither the fold nor active site architecture of the human mARC1 protein.
Authors: Struwe, M.A. / Clement, B. / Scheidig, A.
History
DepositionJul 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Mitochondrial amidoxime-reducing component 1,Endolysin,Mitochondrial amidoxime-reducing component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3885
Polymers50,5461
Non-polymers8424
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-10 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.063, 74.887, 111.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules D

#1: Protein Mitochondrial amidoxime-reducing component 1,Endolysin,Mitochondrial amidoxime-reducing component 1 / mARC1 / Molybdenum cofactor sulfurase C-terminal domain-containing protein 1 / MOSC domain- ...mARC1 / Molybdenum cofactor sulfurase C-terminal domain-containing protein 1 / MOSC domain-containing protein 1 / Moco sulfurase C-terminal domain-containing protein 1 / Lysis protein / Lysozyme / Muramidase / mARC1 / Molybdenum cofactor sulfurase C-terminal domain-containing protein 1 / MOSC domain-containing protein 1 / Moco sulfurase C-terminal domain-containing protein 1


Mass: 50546.078 Da / Num. of mol.: 1 / Mutation: A165T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: MTARC1, MARC1, MOSC1, e, T4Tp126 / Production host: Escherichia coli (E. coli) / Variant (production host): TP1001
References: UniProt: Q5VT66, UniProt: D9IEF7, Oxidoreductases; Acting on other nitrogenous compounds as donors, lysozyme

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Non-polymers , 5 types, 578 molecules

#2: Chemical ChemComp-EFK / oxidanyl(oxidanylidene)molybdenum


Mass: 128.947 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HMoO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MTE / PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER


Mass: 395.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6PS2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 100 mM bis-tris-propane, 5 mM sodium molybdate, 27.5 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.6→53.52 Å / Num. obs: 66911 / % possible obs: 98.6 % / Redundancy: 13.6 % / Biso Wilson estimate: 20.25 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.026 / Rrim(I) all: 0.096 / Net I/σ(I): 21 / Num. measured all: 910173
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.6313.70.2394421032340.9860.0670.2489.197.3
8.76-53.52120.08952694380.9930.0270.0942893.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.34 Å31.92 Å
Translation6.34 Å31.92 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RESOLVEmodel building
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FW2

6fw2


Resolution: 1.6→31.92 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1863 3327 4.98 %
Rwork0.16 63526 -
obs0.1613 66853 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.68 Å2 / Biso mean: 28.6048 Å2 / Biso min: 11.17 Å2
Refinement stepCycle: final / Resolution: 1.6→31.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 1275 574 4070
Biso mean--21.72 35.42 -
Num. residues----368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.620.2211460.17972562270897
1.62-1.650.21261280.17672588271697
1.65-1.670.21871280.16842590271898
1.67-1.70.21091460.1692601274797
1.7-1.730.20321300.17112584271498
1.73-1.760.19361310.16752625275698
1.76-1.790.21071310.17592603273497
1.79-1.830.23281460.1972591273799
1.83-1.870.23041270.18652635276298
1.87-1.910.22811460.17042575272197
1.91-1.960.20711300.17292641277198
1.96-2.020.1881230.1732654277799
2.02-2.080.18631420.17612626276899
2.08-2.140.20191510.17372636278798
2.14-2.220.19131330.16082624275799
2.22-2.310.21941400.16162673281399
2.31-2.410.18381480.15752649279799
2.41-2.540.19921360.15482679281599
2.54-2.70.17091190.1532688280799
2.7-2.910.17381300.15872676280698
2.91-3.20.16271600.155927082868100
3.2-3.660.18061420.148927152857100
3.66-4.610.161420.138627732915100
4.61-31.920.18741720.1672830300298

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