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- PDB-6etf: The Structure of the Mo-insertase domain Cnx1E from Arabidopsis t... -

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Basic information

Entry
Database: PDB / ID: 6etf
TitleThe Structure of the Mo-insertase domain Cnx1E from Arabidopsis thaliana in complex with AMP and molybdate
ComponentsMolybdopterin biosynthesis protein CNX1
KeywordsPLANT PROTEIN / Arabidopsis / Arabidopsis Proteins / Coenzymes / Metalloproteins / Catalytic Domain / Nucleotide Binding / Entropic Enzyme / Adenosine Monophosphate / molybdate / alternate binding / insertion mechanism
Function / homology
Function and homology information


molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / nitrate reductase 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 / Molybdenum cofactor biosynthesis proteins signature 2. / Molybdopterin biosynthesis moea protein, domain 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 / Molybdenum cofactor biosynthesis proteins signature 2. / Molybdopterin biosynthesis moea protein, domain 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
ADENOSINE MONOPHOSPHATE / MOLYBDATE ION / Molybdopterin biosynthesis protein CNX1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.781 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
DepositionOct 26, 2017Deposition 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)50,5438
Polymers49,7631
Non-polymers7807
Water7,692427
1
A: Molybdopterin biosynthesis protein CNX1
hetero molecules

A: Molybdopterin biosynthesis protein CNX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,08616
Polymers99,5262
Non-polymers1,55914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area12200 Å2
ΔGint-53 kcal/mol
Surface area31730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.110, 123.570, 131.790
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-982-

HOH

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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
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) / Strain (production host): RK5204
References: UniProt: Q39054, molybdopterin molybdotransferase, molybdopterin adenylyltransferase

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Non-polymers , 5 types, 434 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / 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-MOO / MOLYBDATE ION / MOLYBDATE / Molybdate


Mass: 159.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: MoO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 % (v/v) 1,2-Ethanediol; 10 % (w/v) PEG 8000; 0.3 M MgCl2; 0.3 M CaCl2; 0.1 M Tris/BICINE, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.77 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2017 / Details: mirrors
RadiationMonochromator: SI111 double crystal with sagital bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 1.781→45.072 Å / Num. obs: 34559 / % possible obs: 65.61 % / Observed criterion σ(I): -3 / Redundancy: 15.38 % / Biso Wilson estimate: 36.87 Å2 / CC1/2: 0.9997 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.014 / Rrim(I) all: 0.056 / Net I/σ(I): 26.558
Reflection shellResolution: 1.781→1.963 Å / Redundancy: 9.72 % / Rmerge(I) obs: 1.339 / Mean I/σ(I) obs: 1.527 / Num. unique obs: 1728 / CC1/2: 0.719 / Rpim(I) all: 0.443 / Rrim(I) all: 1.414 / % possible all: 13.18

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
MxCuBEdata collection
XDSNov 1, 2016data reduction
STARANISO1.0.5data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G2R

5g2r


Resolution: 1.781→33.14 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.166 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.144
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1673 4.84 %RANDOM
Rwork0.173 ---
obs0.175 34550 65.5 %-
Displacement parametersBiso mean: 38.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.1167 Å20 Å20 Å2
2--0.5892 Å20 Å2
3----0.4725 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.781→33.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 45 427 3579
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016550HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2311937HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1437SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes993HARMONIC5
X-RAY DIFFRACTIONt_it6550HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.65
X-RAY DIFFRACTIONt_other_torsion13.53
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_contact7138SEMIHARMONIC4
LS refinement shellResolution: 1.78→1.84 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.4499 -5.88 %
Rwork0.4007 128 -
all0.4038 136 -
obs--3.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7778-0.05150.72620.5539-0.08692.01360.0814-0.23960.13780.2179-0.09590.0041-0.2052-0.2690.0145-0.0587-0.03780.0384-0.0606-0.0387-0.090830.754317.692627.0374
20.61930.0706-0.15240.97640.34811.73710.09160.07940.0784-0.174-0.07510.1195-0.3167-0.0891-0.0165-0.05840.07140.0001-0.07480.0352-0.064726.130320.7559-16.9207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|16 - 192 }
2X-RAY DIFFRACTION2{ A|193 - 442 }

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