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- PDB-6rms: The Structure of variant D274E of the Mo-insertase domain Cnx1E f... -

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Basic information

Entry
Database: PDB / ID: 6rms
TitleThe Structure of variant D274E of the Mo-insertase domain Cnx1E from Arabidopsis thaliana in complex with AMP
ComponentsMolybdopterin biosynthesis protein CNX1
KeywordsPLANT PROTEIN / Arabidopsis / Arabidopsis Proteins / Metalloproteins / Catalytic Domain / Nucleotide Binding / Adenosine Monophosphate
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
ADENOSINE MONOPHOSPHATE / IMIDAZOLE / Molybdopterin biosynthesis protein CNX1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SOLUTION SCATTERING / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsKrausze, J.
CitationJournal: Biosci.Rep. / Year: 2020
Title: Insights into the Cnx1E catalyzed MPT-AMP hydrolysis.
Authors: Hercher, T.W. / Krausze, J. / Hoffmeister, S. / Zwerschke, D. / Lindel, T. / Blankenfeldt, W. / Mendel, R.R. / Kruse, T.
History
DepositionMay 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdopterin biosynthesis protein CNX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0156
Polymers45,4161
Non-polymers5995
Water4,107228
1
A: Molybdopterin biosynthesis protein CNX1
hetero molecules

A: Molybdopterin biosynthesis protein CNX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,03012
Polymers90,8332
Non-polymers1,19710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area9130 Å2
ΔGint-87 kcal/mol
Surface area31480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.836, 119.480, 136.867
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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: 45416.332 Da / Num. of mol.: 1 / Mutation: D274E
Source method: isolated from a genetically manipulated source
Details: OXIDATION OF CYS-161 DUE TO RADIATION DAMGE / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CNX1, At5g20990, F22D1.6, T10F18.20 / Plasmid: PGPUS-CNX1E / Details (production host): pQE-80 erivative / Production host: Escherichia coli (E. coli)
References: UniProt: Q39054, molybdopterin molybdotransferase, molybdopterin adenylyltransferase

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Non-polymers , 6 types, 233 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
SOLUTION SCATTERING

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.56 % / Description: isometric prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12 M 1,6-Hexanediol; 0.12 M 1-Butanol; 0.12 M 1,2-Propanediol (racemic); 0.12 M 2-Propanol; 0.12 M 1,4-Butanediol; 0.12 M 1,3-Propanediol; 30% (v/v) glycerol; 30% (w/v) PEG 4000; 0.1 M ...Details: 0.12 M 1,6-Hexanediol; 0.12 M 1-Butanol; 0.12 M 1,2-Propanediol (racemic); 0.12 M 2-Propanol; 0.12 M 1,4-Butanediol; 0.12 M 1,3-Propanediol; 30% (v/v) glycerol; 30% (w/v) PEG 4000; 0.1 M imidazole; 0.1 M MES; pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 12, 2018 / Details: focussing mirrors
RadiationMonochromator: double crystal (Si-111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.74→90.009 Å / Num. obs: 34702 / % possible obs: 65.7 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 34 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.023 / Rrim(I) all: 0.062 / Net I/σ(I): 25.6
Reflection shellResolution: 1.745→1.905 Å / Redundancy: 13 % / Rmerge(I) obs: 1.605 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1736 / CC1/2: 0.639 / Rpim(I) all: 0.663 / Rrim(I) all: 1.738 / % possible all: 16

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSVERSION Jan 26, 2018data reduction
autoPROC1.0.5data scaling
Aimless0.7.1data scaling
Coot0.8.9.1model building
BUSTER2.10.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ETD

6etd


Resolution: 1.74→23.54 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.136 / SU Rfree Cruickshank DPI: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1723 4.97 %RANDOM
Rwork0.201 ---
obs0.202 34684 63.7 %-
Displacement parametersBiso mean: 43.25 Å2
Baniso -1Baniso -2Baniso -3
1--3.2629 Å20 Å20 Å2
2--3.7856 Å20 Å2
3----0.5227 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 1.74→23.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2923 0 45 228 3196
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016096HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0711117HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1335SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes913HARMONIC5
X-RAY DIFFRACTIONt_it6096HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.53
X-RAY DIFFRACTIONt_other_torsion13.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion421SEMIHARMONIC5
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_contact6350SEMIHARMONIC4
LS refinement shellResolution: 1.74→1.85 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2005 -6.2 %
Rwork0.2607 651 -
all0.2566 694 -
obs--7.57 %
Refinement TLS params.Method: refined / Origin x: 26.3709 Å / Origin y: 19.6888 Å / Origin z: 0.6873 Å
111213212223313233
T-0.0649 Å20.0178 Å20.0103 Å2-0.0371 Å20.0196 Å2---0.0047 Å2
L0.2339 °20.0535 °20.0932 °2-0 °20.0184 °2--0.1999 °2
S0.0195 Å °0.032 Å °0.1436 Å °0.018 Å °0.0293 Å °0.0359 Å °0.0245 Å °-0.0748 Å °-0.0488 Å °
Refinement TLS groupSelection details: { A|* }

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