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- PDB-5erq: Gephyrin E domain at 1.55 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 5erq
TitleGephyrin E domain at 1.55 angstrom resolution
ComponentsGephyrin
KeywordsTRANSFERASE / Molybdenum cofactor / tungsten cofactor / Moco biosynthesis
Function / homology
Function and homology information


Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / gamma-aminobutyric acid receptor clustering / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / nitrate reductase activity ...Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / gamma-aminobutyric acid receptor clustering / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / nitrate reductase activity / postsynaptic specialization / inhibitory synapse / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / postsynaptic neurotransmitter receptor diffusion trapping / response to metal ion / molybdopterin cofactor binding / postsynaptic specialization membrane / neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic specialization, intracellular component / protein targeting / GABA-ergic synapse / synapse assembly / tubulin binding / synaptic membrane / establishment of protein localization / cytoplasmic side of plasma membrane / protein-macromolecule adaptor activity / postsynaptic membrane / postsynapse / molecular adaptor activity / postsynaptic density / cytoskeleton / signaling receptor binding / neuronal cell body / dendrite / ATP binding / identical protein binding / metal ion binding / cytosol / cytoplasm
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
ACETATE ION / Gephyrin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKasaragod, V.B. / Schindelin, H.
CitationJournal: Structure / Year: 2016
Title: Structural Framework for Metal Incorporation during Molybdenum Cofactor Biosynthesis.
Authors: Kasaragod, V.B. / Schindelin, H.
History
DepositionNov 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gephyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,47913
Polymers45,6521
Non-polymers82712
Water9,350519
1
A: Gephyrin
hetero molecules

A: Gephyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,95826
Polymers91,3052
Non-polymers1,65424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_557-x,y,-z+21
Buried area10580 Å2
ΔGint-59 kcal/mol
Surface area35520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.669, 99.287, 113.725
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-1069-

HOH

21A-1284-

HOH

31A-1306-

HOH

41A-1324-

HOH

51A-1334-

HOH

61A-1403-

HOH

71A-1413-

HOH

81A-1417-

HOH

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Components

#1: Protein Gephyrin / Putative glycine receptor-tubulin linker protein


Mass: 45652.395 Da / Num. of mol.: 1 / Fragment: UNP residues 318-736
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gphn, Gph / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q03555, molybdopterin adenylyltransferase, molybdopterin molybdotransferase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M sodium acetate, 25% MPD / PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.55→43 Å / Num. obs: 71703 / % possible obs: 98.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.1
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 1.5 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PD0

4pd0


Resolution: 1.55→40.383 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.187 3553 5 %
Rwork0.1541 --
obs0.1557 71069 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→40.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3181 0 56 519 3756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013437
X-RAY DIFFRACTIONf_angle_d1.3344697
X-RAY DIFFRACTIONf_dihedral_angle_d12.711326
X-RAY DIFFRACTIONf_chiral_restr0.056546
X-RAY DIFFRACTIONf_plane_restr0.008626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.57120.28681430.2772611X-RAY DIFFRACTION98
1.5712-1.59370.24741610.26072658X-RAY DIFFRACTION98
1.5937-1.61750.29931430.25172657X-RAY DIFFRACTION98
1.6175-1.64280.30021320.24852663X-RAY DIFFRACTION98
1.6428-1.66970.24291440.23722663X-RAY DIFFRACTION98
1.6697-1.69850.23591310.22892652X-RAY DIFFRACTION98
1.6985-1.72940.28281390.21622661X-RAY DIFFRACTION98
1.7294-1.76260.22571360.2042687X-RAY DIFFRACTION98
1.7626-1.79860.22911710.19022650X-RAY DIFFRACTION98
1.7986-1.83770.23431300.19242646X-RAY DIFFRACTION97
1.8377-1.88050.20571510.18142665X-RAY DIFFRACTION99
1.8805-1.92750.21951320.17312700X-RAY DIFFRACTION99
1.9275-1.97960.21731360.17012695X-RAY DIFFRACTION99
1.9796-2.03790.16341380.15952692X-RAY DIFFRACTION98
2.0379-2.10360.16561530.14442695X-RAY DIFFRACTION99
2.1036-2.17880.17081250.1492740X-RAY DIFFRACTION99
2.1788-2.2660.14731460.14252690X-RAY DIFFRACTION99
2.266-2.36920.19521470.13982710X-RAY DIFFRACTION98
2.3692-2.4940.17321690.13912701X-RAY DIFFRACTION100
2.494-2.65030.18771270.15152753X-RAY DIFFRACTION99
2.6503-2.85490.17821490.14592719X-RAY DIFFRACTION100
2.8549-3.14210.20091420.14452766X-RAY DIFFRACTION100
3.1421-3.59650.17911400.13092762X-RAY DIFFRACTION99
3.5965-4.53020.15611240.11592814X-RAY DIFFRACTION100
4.5302-40.39690.16671440.15672866X-RAY DIFFRACTION98
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)
11.8848-1.1328-1.78743.59094.30547.13650.03270.0402-0.1156-0.13480.1957-0.22030.05380.4491-0.22370.15440.0471-0.01270.14050.04650.158318.8504130.0945108.0056
21.07130.4523-1.35690.3198-0.49211.81630.0953-0.181-0.04810.0795-0.10070.0423-0.07740.1045-0.00510.1397-0.0198-0.00040.17760.020.1608-2.3492131.1712147.0035
30.8931-0.54671.69140.9866-0.8713.7739-0.06120.16120.0143-0.0838-0.0326-0.0939-0.13640.17540.09240.1379-0.00660.01050.17610.0060.15484.2585139.997893.4894
43.49090.24531.09744.3296-1.52441.7572-0.17570.88710.1628-0.78210.1017-0.13680.07340.33430.02560.2534-0.03030.01050.35080.03450.193817.4244140.655992.6298
53.3008-0.11120.26233.20550.3023.44780.02090.31380.0681-0.28540.0338-0.2785-0.02590.3745-0.02050.13350.02340.04530.22220.00610.161321.4246133.09394.9431
61.54131.39990.32222.2129-0.05940.8245-0.07020.0688-0.1284-0.22680.07150.06340.1973-0.0193-0.00870.21250.0265-0.0110.145-0.01740.21135.438118.6488104.1133
77.8075-5.0654-1.177.0233-0.130.66070.22680.96670.2141-0.6330.02610.90320.0916-0.4184-0.25020.3012-0.0267-0.06190.31590.06130.3474-5.5949117.6357100.4648
83.98492.00382.38672.755-1.07054.38060.03990.1861-0.6103-0.3883-0.0396-0.11470.56620.09790.07790.33670.01260.04550.1275-0.01680.30015.2337109.2908100.04
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 319 through 349 )
2X-RAY DIFFRACTION2chain 'A' and (resid 350 through 506 )
3X-RAY DIFFRACTION3chain 'A' and (resid 507 through 550 )
4X-RAY DIFFRACTION4chain 'A' and (resid 551 through 580 )
5X-RAY DIFFRACTION5chain 'A' and (resid 581 through 627 )
6X-RAY DIFFRACTION6chain 'A' and (resid 628 through 686 )
7X-RAY DIFFRACTION7chain 'A' and (resid 687 through 712 )
8X-RAY DIFFRACTION8chain 'A' and (resid 713 through 736 )

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