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- PDB-6q32: The structure of the Mo-insertase domain Cnx1E (variant S269DD274... -

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Basic information

Entry
Database: PDB / ID: 6q32
TitleThe structure of the Mo-insertase domain Cnx1E (variant S269DD274S) from Arabidopsis thaliana in complex with Moco-AMP
ComponentsMolybdopterin biosynthesis protein CNX1
KeywordsBIOSYNTHETIC PROTEIN / Molybdenum cofactor / Moco biosynthesis / Mo insertase / Moco-AMP / accumulating variant / molybdate binding / hydrolase
Function / homology
Function and homology information


glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / gamma-aminobutyric acid receptor clustering / nitrate reductase activity / auxin-activated signaling pathway / Mo-molybdopterin cofactor biosynthetic process ...glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / gamma-aminobutyric acid receptor clustering / nitrate reductase activity / auxin-activated signaling pathway / Mo-molybdopterin cofactor biosynthetic process / molybdenum ion binding / postsynaptic neurotransmitter receptor diffusion trapping / response to metal ion / dendrite / ATP binding / cytosol
Similarity search - Function
Molybdenum cofactor biosynthesis proteins signature 2. / Molybdenum cofactor biosynthesis proteins signature 1. / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / Molybdenum cofactor biosynthesis, conserved site ...Molybdenum cofactor biosynthesis proteins signature 2. / Molybdenum cofactor biosynthesis proteins signature 1. / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / Molybdenum cofactor biosynthesis, conserved site / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain
Similarity search - Domain/homology
Moco-AMP / TRIETHYLENE GLYCOL / Molybdopterin biosynthesis protein CNX1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsKrausze, J.
CitationJournal: Nat.Chem. / Year: 2021
Title: Mechanism of molybdate insertion into pterin-based molybdenum cofactors.
Authors: Probst, C. / Yang, J. / Krausze, J. / Hercher, T.W. / Richers, C.P. / Spatzal, T. / Kc, K. / Giles, L.J. / Rees, D.C. / Mendel, R.R. / Kirk, M.L. / Kruse, T.
History
DepositionDec 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 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
A: Molybdopterin biosynthesis protein CNX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0015
Polymers49,7631
Non-polymers1,2384
Water7,837435
1
A: Molybdopterin biosynthesis protein CNX1
hetero molecules

A: Molybdopterin biosynthesis protein CNX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,00310
Polymers99,5262
Non-polymers2,4768
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area9620 Å2
ΔGint-56 kcal/mol
Surface area32360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.010, 123.290, 133.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-504-

PGE

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Molybdopterin biosynthesis protein CNX1 / Molybdenum cofactor biosynthesis enzyme CNX1


Mass: 49763.094 Da / Num. of mol.: 1 / Mutation: S269D, D274S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CNX1, At5g20990, F22D1.6, T10F18.20 / Plasmid: PGPLUS-CNX1E / Details (production host): pQE80 derivative / Production host: Escherichia coli (E. coli) / Variant (production host): RK5206
References: UniProt: Q39054, molybdopterin molybdotransferase, molybdopterin adenylyltransferase

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Non-polymers , 5 types, 439 molecules

#2: Chemical ChemComp-NWS / Moco-AMP


Mass: 868.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26MoN10O15P2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.69 Å3/Da / Density % sol: 54.27 % / Description: ISOMETRIC TETRAGONAL PRISM
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 24 % (v/v) PEG 400; in an anoxic atmosphere containing a 95 % argon and 5 % hydrogen gas

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
31001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-210.99987
SYNCHROTRONSSRL BL12-220.99987
SYNCHROTRONSSRL BL12-231.74262
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELOct 2, 2014Rh coated collimating mirrors, K-B focusing mirrors
DECTRIS PILATUS 6M2PIXELOct 2, 2014Rh coated collimating mirrors, K-B focusing mirrors
DECTRIS PILATUS 6M3PIXELOct 2, 2014Rh coated collimating mirrors, K-B focusing mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Liquid nitrogen-cooled double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Liquid nitrogen-cooled double crystal Si(111)SINGLE WAVELENGTHMx-ray2
3Liquid nitrogen-cooled double crystal Si(111)SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.999871
21.742621
31
Reflection

Biso Wilson estimate: 21.97 Å2 / Entry-ID: 6Q32 / Observed criterion σ(I): -3

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
1.39-39.267801569613.30.9990.0550.0220.059124.1
1.386-20.321067669913.10.9910.18460.1919216.05
2.061-20.344097839912.40.9920.15470.1611353.62
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-ID% possible all
1.39-1.488122.0281.340070.4450.8772.215169.8
1.386-1.4410.16.1110.18101780.1166.44296
2.061-2.1359.10.395929520.9450.4219390

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
STARANISOdata scaling
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G2S

5g2s


Resolution: 1.39→20.35 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU R Cruickshank DPI: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.061 / SU Rfree Blow DPI: 0.06 / SU Rfree Cruickshank DPI: 0.058
RfactorNum. reflection% reflectionSelection details
Rfree0.177 3902 4.87 %RANDOM
Rwork0.159 ---
obs0.16 80115 74.6 %-
Displacement parametersBiso mean: 27.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.0434 Å20 Å20 Å2
2--0.9461 Å20 Å2
3---0.0973 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: 1 / Resolution: 1.39→20.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 73 435 3615
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016552HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1311948HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1441SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes990HARMONIC5
X-RAY DIFFRACTIONt_it6552HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.46
X-RAY DIFFRACTIONt_other_torsion12.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion450SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7466SEMIHARMONIC4
LS refinement shellResolution: 1.39→1.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 -3.19 %
Rwork0.2877 546 -
all0.2869 564 -
obs--7.24 %
Refinement TLS params.Method: refined / Origin x: 5.8853 Å / Origin y: 42.2335 Å / Origin z: 1.1382 Å
111213212223313233
T-0.0789 Å20.0072 Å2-0.0125 Å2--0.0724 Å20.0105 Å2---0.0306 Å2
L0.3401 °2-0.0141 °2-0.1098 °2-0.3087 °2-0.0075 °2--0.9089 °2
S0.0487 Å °-0.0173 Å °-0.088 Å °0.0073 Å °-0.0515 Å °-0.0171 Å °0.1512 Å °0.0267 Å °0.0028 Å °
Refinement TLS groupSelection details: { A|* }

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