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- PDB-6fw2: Crystal Structure of human mARC1 -

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Basic information

Entry
Database: PDB / ID: 6fw2
TitleCrystal Structure of human mARC1
ComponentsMitochondrial amidoxime-reducing component 1,Endolysin,Mitochondrial amidoxime-reducing component 1
KeywordsOXIDOREDUCTASE / mARC / MOSC / molybdenum cofactor / Moco / N-reduction
Function / homology
Function and homology information


nitrate metabolic process / nitric-oxide synthase complex / detoxification of nitrogen compound / 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 / nitrite reductase activity ...nitrate metabolic process / nitric-oxide synthase complex / detoxification of nitrogen compound / 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 / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / 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 / MOSC domain / Molybdenum cofactor sulfurase, C-terminal / MOSC domain profile. / Pyruvate kinase-like, insert domain superfamily / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily ...MOSC, N-terminal beta barrel / MOSC N-terminal beta barrel domain / MOSC domain / Molybdenum cofactor sulfurase, C-terminal / MOSC domain profile. / Pyruvate kinase-like, insert domain superfamily / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
oxidanyl(oxidanylidene)molybdenum / MOLYBDATE ION / Chem-MTE / PHOSPHATE ION / Endolysin / Mitochondrial amidoxime-reducing component 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsKubitza, C. / Scheidig, A.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Crystal structure of human mARC1 reveals its exceptional position among eukaryotic molybdenum enzymes.
Authors: Kubitza, C. / Bittner, F. / Ginsel, C. / Havemeyer, A. / Clement, B. / Scheidig, A.J.
History
DepositionMar 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,3879
Polymers51,8451
Non-polymers1,5418
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-17 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.133, 74.818, 110.726
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 A

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


Mass: 51845.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: MARC1, MOSC1, e, T4Tp126 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): TP1000
References: UniProt: Q5VT66, UniProt: D9IEF7, Oxidoreductases, lysozyme

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Non-polymers , 6 types, 447 molecules

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


Mass: 128.947 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HMoO2
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


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


Mass: 159.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: MoO4
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O

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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: 49.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Bis-TRIS propane, Na2MoO4, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.78→43.57 Å / Num. obs: 45538 / % possible obs: 91.9 % / Redundancy: 6.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.034 / Rrim(I) all: 0.091 / Net I/σ(I): 10.9
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.418 / Num. unique obs: 664 / CC1/2: 0.829 / Rpim(I) all: 0.217 / Rrim(I) all: 0.473 / % possible all: 23.9

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→43.57 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / Matrix type: sparse / SU B: 0.003 / SU ML: 0 / SU R Cruickshank DPI: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.119 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 2288 5 %RANDOM
Rwork0.1694 ---
obs0.1714 45386 91.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 137.61 Å2 / Biso mean: 29.685 Å2 / Biso min: 10.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å20 Å2
2---0.68 Å2-0 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.78→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3509 0 71 439 4019
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.778-1.8240.346500.271071360331.1130.26
1.824-1.8740.2911220.2412586353076.7140.227
1.874-1.9280.2711640.2052990341392.4110.194
1.928-1.9870.2261710.1833114336097.7680.172
1.987-2.0530.2341680.1732988322197.9820.164
2.053-2.1240.1941480.1782944314398.3770.169
2.124-2.2050.221420.1742849303598.550.167
2.205-2.2940.2361660.1712702290598.7260.166
2.294-2.3960.2031280.1682628279098.7810.164
2.396-2.5130.291320.1832533269298.9970.181
2.513-2.6490.2321320.1812404256298.9850.182
2.649-2.8090.2151160.1782291243199.0130.18
2.809-3.0030.2251020.1782187230199.4780.182
3.003-3.2430.2241020.1712003213798.5030.176
3.243-3.5510.2071030.1631802196397.0450.173
3.551-3.9690.168880.1511707180199.6670.162
3.969-4.580.147850.1321509159799.8120.146
4.58-5.6010.193640.1381310137899.710.154
5.601-7.8890.176770.182988108598.1570.198
7.889-61.9930.156280.18349265679.2680.202

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