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- PDB-6gbf: The Structure of variant R369A of the Mo-insertase domain Cnx1E f... -

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Basic information

Entry
Database: PDB / ID: 6gbf
TitleThe Structure of variant R369A of the Mo-insertase domain Cnx1E from Arabidopsis thaliana in complex with AMP
ComponentsMolybdopterin biosynthesis protein CNX1
KeywordsTRANSFERASE / Arabidopsis / Arabidopsis Proteins / Coenzymes / Metalloproteins / Catalytic Domain / Nucleotide Binding / Entropic Enzyme / Adenosine Monophosphate
Function / homology
Function and homology information


molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / molybdopterin molybdotransferase / nitrate reductase activity / molybdopterin molybdotransferase activity / auxin-activated signaling pathway / molybdenum ion binding / Mo-molybdopterin cofactor biosynthetic process / response to metal ion / ATP binding
Similarity search - Function
Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdopterin biosynthesis moea protein, domain 2 / 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 ...Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdopterin biosynthesis moea protein, domain 2 / 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) / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis, conserved site / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / Beta Complex / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / Molybdopterin biosynthesis protein CNX1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.712 Å
AuthorsKrausze, J.
CitationJournal: Biochem. J. / Year: 2018
Title: The functional principle of eukaryotic molybdenum insertases.
Authors: Krausze, J. / Hercher, T.W. / Zwerschke, D. / Kirk, M.L. / Blankenfeldt, W. / Mendel, R.R. / Kruse, T.
History
DepositionApr 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 / 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)49,4868
Polymers48,8131
Non-polymers6737
Water7,134396
1
A: Molybdopterin biosynthesis protein CNX1
hetero molecules

A: Molybdopterin biosynthesis protein CNX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,97216
Polymers97,6262
Non-polymers1,34614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area12060 Å2
ΔGint-61 kcal/mol
Surface area31910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.030, 123.970, 132.680
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: 48813.090 Da / Num. of mol.: 1 / Mutation: R369A
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): RK5204
References: UniProt: Q39054, molybdopterin molybdotransferase, molybdopterin adenylyltransferase

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Non-polymers , 5 types, 403 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.64 Å3/Da / Density % sol: 53.52 % / Description: isometric tetragonal prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M imidazole, 0.1 M MES pH 6.5; 0.06 M sodium nitrate, 0.06 M sodium phosphate, 0.06 M ammonium sulfate; 20 % (v/v) PEG 500 MME, 10 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2017 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.712→66.34 Å / Num. obs: 42230 / % possible obs: 71.7 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 28.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.034 / Rrim(I) all: 0.054 / Net I/σ(I): 16.9
Reflection shellResolution: 1.712→1.849 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2113 / CC1/2: 0.615 / Rpim(I) all: 0.665 / Rrim(I) all: 1.022 / % possible all: 17.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSJun 1, 2017data reduction
STARANISO1.10.9data scaling
PHASER2.8.1phasing
Coot0.8.9model building
autoBUSTER2.10.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G2R

5g2r


Resolution: 1.712→25.07 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.126 / SU Rfree Blow DPI: 0.115 / SU Rfree Cruickshank DPI: 0.111
Details: The data were corrected for anisotropy prior to refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2121 5.03 %RANDOM
Rwork0.173 ---
obs0.174 42206 71.6 %-
Displacement parametersBiso mean: 33.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.0848 Å20 Å20 Å2
2--0.9342 Å20 Å2
3----0.8494 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.712→25.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3083 0 51 396 3530
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016488HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0711819HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1424SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes992HARMONIC5
X-RAY DIFFRACTIONt_it6488HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.71
X-RAY DIFFRACTIONt_other_torsion13.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion443SEMIHARMONIC5
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_contact7010SEMIHARMONIC4
LS refinement shellResolution: 1.71→1.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1749 -6.05 %
Rwork0.2346 264 -
all0.2309 281 -
obs--6.45 %
Refinement TLS params.Method: refined / Origin x: 27.1825 Å / Origin y: 19.543 Å / Origin z: 1.1463 Å
111213212223313233
T-0.0864 Å20.0188 Å20.0229 Å2--0.0824 Å20 Å2---0.0523 Å2
L0.3195 °20.0271 °20.1315 °2-0.365 °20.0326 °2--1.0602 °2
S0.0524 Å °-0.0101 Å °0.0885 Å °-0.0002 Å °-0.0206 Å °0.0342 Å °-0.1981 Å °-0.0693 Å °-0.0318 Å °
Refinement TLS groupSelection details: { A|* }

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