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- PDB-1o8n: The active site of the molybdenum cofactor biosynthetic protein d... -

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Basic information

Entry
Database: PDB / ID: 1o8n
TitleThe active site of the molybdenum cofactor biosynthetic protein domain Cnx1G
ComponentsMOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN
KeywordsMOLYBDENUM COFACTOR BIOSYNTHESIS / CNX1G / MUTANTS
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
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-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Molybdopterin biosynthesis protein CNX1
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKuper, J. / Winking, J. / Hecht, H.J. / Schwarz, G. / Mendel, R.R.
CitationJournal: Arch.Biochem.Biophys. / Year: 2003
Title: The Active Site of the Molybdenum Cofactor Biosynthetic Protein Domain Cnx1G
Authors: Kuper, J. / Winking, J. / Hecht, H.J. / Mendel, R.R. / Schwarz, G.
History
DepositionNov 28, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN
B: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN
C: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)53,0563
Polymers53,0563
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)122.486, 122.486, 174.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPROAA4 - 284 - 28
21PROPROPROPROBB4 - 284 - 28
31PROPROPROPROCC4 - 284 - 28
12ALAALAALAALAAA30 - 4430 - 44
22ALAALAALAALABB30 - 4430 - 44
32ALAALAALAALACC30 - 4430 - 44
13VALVALILEILEAA46 - 16246 - 162
23VALVALILEILEBB46 - 16246 - 162
33VALVALILEILECC46 - 16246 - 162

NCS oper:
IDCodeMatrixVector
1given(0.491908, 0.630518, 0.600395), (-0.360731, -0.480023, 0.799657), (0.792401, -0.609939, -0.008679)53.6071, 44.8248, -84.9782
2given(0.496506, -0.378581, 0.781126), (0.621857, -0.472707, -0.624373), (0.605619, 0.795754, 0.000722)-3.615, 110.0926, -14.4515

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Components

#1: Protein MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN / MOLYBDENUM COFACTOR / BIOSYNTHESIS ENZYME CNX1


Mass: 17685.492 Da / Num. of mol.: 3 / Fragment: CNX1 G-DOMAIN, RESIDUES 462-628 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Strain: CV. COLUMBIA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RK5206 / References: UniProt: Q39054
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN A, THR 542 ALA ENGINEERED MUTATION IN CHAIN B, THR 542 ALA ENGINEERED ...ENGINEERED MUTATION IN CHAIN A, THR 542 ALA ENGINEERED MUTATION IN CHAIN B, THR 542 ALA ENGINEERED MUTATION IN CHAIN C, THR 542 ALA THE MOLECULE CNX1G IS INVOLVED IN MOLYBDENUM COFACTOR BIOSYNTHESIS
Sequence detailsDOMAIN DEFINITION MODIFIED FROM SWALL:CNX1_ARATH_2 N-TERMINAL EXTENSION VPGP, C-TERMINAL EXTENSION KQIKGDK

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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: 2.9 Å3/Da / Density % sol: 56.5 %
Crystal growpH: 6.5
Details: 1.4 M SODIUM ACETATE 0.1 M SODIUM CACODYLATE, PH 6.5
Crystal grow
*PLUS
Method: unknown / Details: Schwarz, G., (2001) J. Mol. Biol., 312, 405.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jul 18, 2001 / Details: OSMIX MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→87.71 Å / Num. obs: 15774 / % possible obs: 99.7 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 4.4 / % possible all: 100
Reflection
*PLUS
Num. obs: 16631
Reflection shell
*PLUS
% possible obs: 100 % / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EAV

1eav


Resolution: 2.8→100 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 10.964 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.945 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 844 5.1 %RANDOM
Rwork0.194 ---
obs0.196 15773 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3582 0 0 49 3631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223633
X-RAY DIFFRACTIONr_bond_other_d0.0020.023516
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9984923
X-RAY DIFFRACTIONr_angle_other_deg0.84638211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0015483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023978
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02612
X-RAY DIFFRACTIONr_nbd_refined0.2310.2765
X-RAY DIFFRACTIONr_nbd_other0.2490.23940
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.22140
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8011.52421
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57523912
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.18131212
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1714.51011
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2290 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.170.5
2Bmedium positional0.170.5
3Cmedium positional0.220.5
1Amedium thermal0.42
2Bmedium thermal0.472
3Cmedium thermal0.462
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.372 69
Rwork0.289 1128
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 87.71 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.49
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg5
X-RAY DIFFRACTIONr_plane_restr0.004

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