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- PDB-5err: GephE in complex with Mg(2+) - ADP -

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Basic information

Entry
Database: PDB / ID: 5err
TitleGephE in complex with Mg(2+) - ADP
ComponentsGephyrin
KeywordsTRANSFERASE / molybdenum and tungsten cofactor / Moco / Wco / terminal step
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 / postsynaptic specialization ...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 / postsynaptic specialization / nitrate reductase activity / inhibitory synapse / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / postsynaptic neurotransmitter receptor diffusion trapping / postsynaptic specialization membrane / response to metal ion / molybdopterin cofactor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic specialization, intracellular component / GABA-ergic synapse / protein targeting / synapse assembly / tubulin binding / synaptic membrane / establishment of protein localization / cytoplasmic side of plasma membrane / protein-macromolecule adaptor activity / postsynaptic membrane / postsynapse / postsynaptic density / molecular adaptor activity / cytoskeleton / signaling receptor binding / dendrite / neuronal cell body / 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 / ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Gephyrin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKasaragod, V.B. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSchi425/8-1 Germany
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 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)47,05014
Polymers45,6521
Non-polymers1,39813
Water8,467470
1
A: Gephyrin
hetero molecules

A: Gephyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,10028
Polymers91,3052
Non-polymers2,79626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_659-x+1,y,-z+41
Unit cell
Length a, b, c (Å)87.681, 99.534, 113.029
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-810-

MPD

21A-1050-

HOH

31A-1256-

HOH

41A-1292-

HOH

51A-1311-

HOH

61A-1368-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 483 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M sodium acetate, 20 % MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.964 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 1.65→43.841 Å / Num. obs: 59012 / % possible obs: 99 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 1.7 / % possible all: 98.1

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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: 1.65→43.841 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1834 2884 4.89 %
Rwork0.1567 --
obs0.158 59011 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→43.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 0 90 470 3716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063459
X-RAY DIFFRACTIONf_angle_d1.1494737
X-RAY DIFFRACTIONf_dihedral_angle_d14.8351346
X-RAY DIFFRACTIONf_chiral_restr0.04548
X-RAY DIFFRACTIONf_plane_restr0.006618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.67710.32641480.26892612X-RAY DIFFRACTION98
1.6771-1.7060.26971260.25332635X-RAY DIFFRACTION98
1.706-1.7370.31411310.25722619X-RAY DIFFRACTION98
1.737-1.77040.26151400.22512628X-RAY DIFFRACTION98
1.7704-1.80660.26171310.21212606X-RAY DIFFRACTION98
1.8066-1.84580.22461250.19832660X-RAY DIFFRACTION98
1.8458-1.88880.22431320.19192630X-RAY DIFFRACTION98
1.8888-1.9360.2021320.17642659X-RAY DIFFRACTION99
1.936-1.98840.18481290.17742645X-RAY DIFFRACTION99
1.9884-2.04690.1811360.15872652X-RAY DIFFRACTION99
2.0469-2.11290.18081360.15492643X-RAY DIFFRACTION99
2.1129-2.18840.20391340.14962669X-RAY DIFFRACTION99
2.1884-2.27610.1671420.14432646X-RAY DIFFRACTION99
2.2761-2.37960.15221470.13712672X-RAY DIFFRACTION99
2.3796-2.50510.15631370.1422696X-RAY DIFFRACTION99
2.5051-2.6620.18521560.15012674X-RAY DIFFRACTION99
2.662-2.86750.15371400.14772691X-RAY DIFFRACTION99
2.8675-3.1560.16611200.14722742X-RAY DIFFRACTION100
3.156-3.61250.16631470.14352727X-RAY DIFFRACTION100
3.6125-4.55060.16811250.12552769X-RAY DIFFRACTION100
4.5506-43.8560.17721700.15852852X-RAY DIFFRACTION100
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)
10.6295-0.2930.98621.8155-2.42375.71920.0546-0.02540.0665-0.03210.08760.1409-0.1296-0.3213-0.13910.09530.02590.01270.1162-0.0190.127326.263118.3926223.8184
23.8861.87772.87371.00051.28281.64110.3963-0.3802-0.03470.3031-0.2816-0.0580.2754-0.2322-0.09780.2406-0.0859-0.02280.2838-0.01260.16251.622819.0633270.0471
34.89952.0533.84760.44841.44163.3420.1589-0.1648-0.00160.0812-0.165-0.09290.0428-0.03150.06460.1961-0.0226-0.03550.1959-0.01940.214949.819421.608265.763
40.2663-0.0111-0.50460.1860.32843.6649-0.00430.0525-0.0102-0.0321-0.02830.00870.0585-0.08340.04350.09820.0116-0.00570.0874-0.00150.102737.058410.1726218.0167
51.9390.2501-0.12942.1827-0.08251.4922-0.03320.2473-0.0743-0.27160.02460.19120.0034-0.23820.00140.12220.0147-0.01640.1504-0.00430.123225.531314.6599208.0334
60.69530.97530.15983.1093-0.41571.7681-0.07240.12940.0656-0.20290.0818-0.2558-0.24520.21390.01110.20410.0070.00060.1363-0.01060.17543.581133.1101216.0934
73.58632.5559-1.40331.93550.04395.2741-0.00310.10.53-0.413-0.10150.231-0.4710.07860.09060.29640.0075-0.03220.11020.00420.285438.863638.655213.058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 319 through 359 )
2X-RAY DIFFRACTION2chain 'A' and (resid 360 through 434 )
3X-RAY DIFFRACTION3chain 'A' and (resid 435 through 472 )
4X-RAY DIFFRACTION4chain 'A' and (resid 473 through 550 )
5X-RAY DIFFRACTION5chain 'A' and (resid 551 through 646 )
6X-RAY DIFFRACTION6chain 'A' and (resid 647 through 712 )
7X-RAY DIFFRACTION7chain 'A' and (resid 713 through 736 )

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