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- PDB-1eav: Crystal Structures of Human Gephyrin and Plant Cnx1 G domains - C... -

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Basic information

Entry
Database: PDB / ID: 1eav
TitleCrystal Structures of Human Gephyrin and Plant Cnx1 G domains - Comparative Analysis and Functional Implications
ComponentsMOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN
KeywordsMOLYBDENUM COFACTOR BIOSYNTHESIS / CNX1G
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 / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsSchwarz, G. / Schrader, N. / Mendel, R.R. / Hecht, H.J.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal Structures of Human Gephyrin and Plant Cnx1 G Domains: Comparative Analysis and Functional Implications
Authors: Schwarz, G. / Schrader, N. / Mendel, R.R. / Hecht, H.J. / Schindelin, H.
History
DepositionJul 17, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 10, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)139,2748
Polymers139,2748
Non-polymers00
Water91951
1
A: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN
B: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN
C: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)52,2283
Polymers52,2283
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)52,2283
Polymers52,2283
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)52,2283
Polymers52,2283
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_564y,z+1,x-11
crystal symmetry operation5_654z+1,x,y-11
MethodPQS
4
H: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN

H: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN

H: MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)52,2283
Polymers52,2283
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
MethodPQS
Unit cell
Length a, b, c (Å)175.303, 175.303, 175.303
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99999, -0.00106, -0.00433), (-0.00105, 0.999997, -0.002159), (0.004332, -0.002154, -0.999988)350.59839, -2.0577, 3.217
2given(0.003418, -0.999988, -0.003362), (0.002298, 0.00337, -0.999992), (0.999991, 0.00341, 0.00231)172.1124, 262.5217, 90.3371
3given(0.001448, -0.001895, 0.999997), (0.99998, 0.006197, -0.001436), (-0.006195, 0.999979, 0.001904)85.2368, 84.9261, -175.2251
4given(7.6E-5, -0.999999, -0.00092), (0.999998, 7.4E-5, 0.001969), (-0.001969, -0.00092, 0.999998)43.8829, 304.35809, -43.973
5given(-0.003358, 0.002114, 0.999992), (-0.000168, 0.999998, -0.002114), (-0.999994, -0.000175, -0.003357)219.77029, -44.1696, -216.2935
6given(-0.999992, -0.004053, -0.000234), (0.000221, 0.003408, -0.999994), (0.004054, -0.999986, -0.003407)391.80331, 131.763, 131.4751
7given(0.999988, 0.0045, 0.001844), (0.001836, 0.001705, -0.999997), (-0.004503, 0.999988, 0.001697)41.1407, 128.2473, 133.4035

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Components

#1: Protein
MOLYBDOPTERIN BIOSYNTHESIS CNX1 PROTEIN / CNX1G / MOLYBDENUM COFACTOR BIOSYNTHESIS ENZYME


Mass: 17409.195 Da / Num. of mol.: 8 / Fragment: CNX1 G-DOMAIN RESIDUES 462-623
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Strain: CV. COLUMBIA / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): DL41 / References: UniProt: Q39054
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE MOLECULE CNX1G IS INVOLVED IN MOLYBDENUM COFACTOR BIOSYNTHESIS
Has protein modificationY
Sequence detailsDOMAIN DEFINITION MODIFIED FROM SWALL:CNX1_ARATH_2 N-TERMIANL EXTENSION VPGP, C-TERMINAL EXTENSION KQI

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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: 3.3 Å3/Da / Density % sol: 61.84 %
Crystal growpH: 6.5
Details: 1.4 M SODIUM ACETATE 0.1 M SODIUM CACODYLATE, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9790, 0.97940, 0.9500, 1.0448
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2000 / Details: PLANAR MIRROR AND TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97941
30.951
41.04481
ReflectionResolution: 2.6→27 Å / Num. obs: 47553 / % possible obs: 90.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 4.7
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 4.3 / % possible all: 75.5

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Processing

Software
NameVersionClassification
REFMAC5.0.36refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→27 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.72 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 0.607 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2582 5.2 %RANDOM
Rwork0.223 ---
obs-47553 90.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Refinement stepCycle: LAST / Resolution: 2.6→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9450 0 0 51 9501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0229586
X-RAY DIFFRACTIONr_bond_other_d0.0020.029280
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg2.4991.99613010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1.112321664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1310.21592
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210468
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021616
X-RAY DIFFRACTIONr_nbd_refined0.2820.32361
X-RAY DIFFRACTIONr_nbd_other0.250.39786
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.5503
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3450.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.368
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2721.56370
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.403210330
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.65533216
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.4034.52680
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
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.388 140
Rwork0.33 2834

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