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- PDB-1o8q: The active site of the molybdenum cofactor biosenthetic protein d... -

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Basic information

Entry
Database: PDB / ID: 1o8q
TitleThe active site of the molybdenum cofactor biosenthetic 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 / 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
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: 2.6 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
D: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN
E: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN
F: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN
G: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN
H: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)141,5968
Polymers141,5968
Non-polymers00
Water8,773487
1
A: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN
B: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN
C: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)53,0993
Polymers53,0993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN
E: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN
F: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)53,0993
Polymers53,0993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
G: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN

G: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN

G: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)53,0993
Polymers53,0993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
MethodPQS
4
H: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN

H: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN

H: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)53,0993
Polymers53,0993
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_564z,x+1,y-11
crystal symmetry operation9_465y-1,z+1,x1
MethodPQS
Unit cell
Length a, b, c (Å)174.610, 174.610, 174.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11H
21A
31B
41C
51D
61E
71F
81G

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 1 / Auth seq-ID: 5 - 162 / Label seq-ID: 5 - 162

Dom-IDAuth asym-IDLabel asym-ID
1HH
2AA
3BB
4CC
5DD
6EE
7FF
8GG

NCS oper:
IDCodeMatrixVector
1given(-0.999987, 0.004999, 0.001269), (0.001283, 0.002847, 0.999995), (0.004996, 0.999983, -0.002854)-41.3455, 130.64169, -130.88071
2given(-0.001751, -0.000155, 0.999998), (0.002733, 0.999996, 0.00016), (-0.999995, 0.002733, -0.00175)-41.7171, -43.5852, 43.718
3given(0.005984, 0.999974, -0.004021), (-0.999978, 0.005972, -0.002991), (-0.002967, 0.004039, 0.999987)133.3987, 130.1187, 44.1124
4given(-0.005684, 0.999973, 0.00462), (-0.001531, 0.004611, -0.999988), (-0.999983, -0.005692, 0.001504)0.021, 171.42281, 177.0338
5given(-0.003959, 0.008938, -0.999952), (-0.99999, -0.002048, 0.00394), (-0.002013, 0.999958, 0.008946)174.3573, 172.7847, 1.8869
6given(-0.999973, -0.006772, 0.002905), (-0.006758, 0.999965, 0.004831), (-0.002938, 0.004812, -0.999984)0.8807, -2.3692, 1.6194
7given(0.99996, 0.008452, 0.002775), (0.002788, -0.001601, -0.999995), (-0.008448, 0.999963, -0.001624)40.7709, 129.1317, 133.22881

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Components

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


Mass: 17699.518 Da / Num. of mol.: 8 / 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


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN A, SER 573 ALA ENGINEERED MUTATION IN CHAIN B, SER 573 ALA ENGINEERED ...ENGINEERED MUTATION IN CHAIN A, SER 573 ALA ENGINEERED MUTATION IN CHAIN B, SER 573 ALA ENGINEERED MUTATION IN CHAIN C, SER 573 ALA ENGINEERED MUTATION IN CHAIN D, SER 573 ALA ENGINEERED MUTATION IN CHAIN E, SER 573 ALA ENGINEERED MUTATION IN CHAIN F, SER 573 ALA ENGINEERED MUTATION IN CHAIN G, SER 573 ALA ENGINEERED MUTATION IN CHAIN H, SER 573 ALA THE MOLECULE CNX1G IS INVOLVED IN MOLYBDENUM COFACTOR BIOSYNTHESIS
Sequence detailsDOMAIN DEFINITION MODIFIED FROM SWALL:CNX1_ARATH_2 N-TERMIANL 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: 57.3 %
Crystal growpH: 7.7 / Details: 2.4 M SODIUM FORMIATE, pH 7.70
Crystal grow
*PLUS
Method: unknown / Details: Schwarz, G., (2001) J. Mol. Biol., 312, 405.
Components of the solutions
*PLUS
Conc.: 2.4 M / Common name: sodium formate

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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: Apr 15, 2002 / Details: OSMIX MIRROR OPTICS
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→43.85 Å / Num. obs: 53034 / % possible obs: 97.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 7.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 4.3 / % possible all: 90.6
Reflection
*PLUS
Highest resolution: 2.6 Å
Reflection shell
*PLUS
% possible obs: 90.6 % / Mean I/σ(I) obs: 3.3

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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: 2.6→43.85 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.369 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.499 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2680 5.1 %RANDOM
Rwork0.193 ---
obs0.195 50319 97 %-
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: 42.45 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9440 0 0 487 9927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229568
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.99512968
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31851264
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_restr0.0860.21592
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026880
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.24706
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2531
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.294
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8691.56344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.771210272
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.93133224
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4754.52696
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: 1170 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Htight positional0.030.05
2Atight positional0.030.05
3Btight positional0.030.05
4Ctight positional0.030.05
5Dtight positional0.030.05
6Etight positional0.030.05
7Ftight positional0.030.05
8Gtight positional0.030.05
1Htight thermal0.090.5
2Atight thermal0.070.5
3Btight thermal0.080.5
4Ctight thermal0.080.5
5Dtight thermal0.080.5
6Etight thermal0.080.5
7Ftight thermal0.080.5
8Gtight thermal0.080.5
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.312 208
Rwork0.26 3370
Refinement
*PLUS
Highest resolution: 2.6 Å / Num. reflection obs: 50292 / % reflection Rfree: 5 % / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.195
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_deg1.389
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg5.318
X-RAY DIFFRACTIONr_plane_restr0.004

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