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- PDB-5ert: GephE in complex with Mn(2+) - ADP -

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Basic information

Entry
Database: PDB / ID: 5ert
TitleGephE in complex with Mn(2+) - ADP
ComponentsGephyrin
KeywordsTRANSFERASE / Moco / Wco / Moco biosyntheis / ADP complex / Manganese
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 / 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 / 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 / ADENOSINE-5'-DIPHOSPHATE / : / PHOSPHATE ION / Gephyrin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)46,67510
Polymers45,6521
Non-polymers1,0229
Water6,161342
1
A: Gephyrin
hetero molecules

A: Gephyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,34920
Polymers91,3052
Non-polymers2,04518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_759-x+2,y,-z+41
Unit cell
Length a, b, c (Å)87.440, 99.090, 111.895
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-904-

HOH

21A-1184-

HOH

31A-1191-

HOH

41A-1210-

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) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q03555, molybdopterin adenylyltransferase, molybdopterin molybdotransferase

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Non-polymers , 6 types, 351 molecules

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


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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M sodium acetate, 26% 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: 2→43.96 Å / Num. obs: 33205 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.195 / Net I/σ(I): 11.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.589 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

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

4pd0


Resolution: 2→42.558 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 1672 5.04 %
Rwork0.1751 --
obs0.1766 33204 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→42.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 59 342 3565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053338
X-RAY DIFFRACTIONf_angle_d0.9944561
X-RAY DIFFRACTIONf_dihedral_angle_d15.4211277
X-RAY DIFFRACTIONf_chiral_restr0.034532
X-RAY DIFFRACTIONf_plane_restr0.004596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05890.26031440.26032609X-RAY DIFFRACTION100
2.0589-2.12530.29411350.24462576X-RAY DIFFRACTION100
2.1253-2.20130.25571360.23232599X-RAY DIFFRACTION100
2.2013-2.28940.23421270.22692612X-RAY DIFFRACTION100
2.2894-2.39360.24851550.20312584X-RAY DIFFRACTION100
2.3936-2.51980.24931480.20152587X-RAY DIFFRACTION100
2.5198-2.67760.23761430.19742611X-RAY DIFFRACTION100
2.6776-2.88430.19141340.18142633X-RAY DIFFRACTION100
2.8843-3.17450.22711520.17242598X-RAY DIFFRACTION100
3.1745-3.63360.19351240.14912661X-RAY DIFFRACTION100
3.6336-4.57710.18321210.12832698X-RAY DIFFRACTION100
4.5771-42.56810.14541530.15982764X-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)
11.6667-0.4826-1.13492.60132.60586.12770.1270.015-0.0685-0.10910.0374-0.22490.15030.3682-0.14770.15070.0266-0.01870.12590.04680.1889105.0209130.7673221.8099
24.00742.3015-2.94461.4769-1.69112.440.4917-0.5680.24020.4008-0.31380.1407-0.29170.3137-0.16920.3033-0.10390.02390.30670.00150.223580.1385129.6465267.5627
34.85012.0939-3.93580.7753-1.54494.94320.3669-0.49880.18660.2031-0.26770.1999-0.3740.2458-0.01750.2673-0.03180.040.1978-0.00820.293581.7796127.3455263.4073
40.1399-0.01490.16930.1218-0.44263.37070.0346-0.00150.0319-0.0179-0.03650.00060.0120.12470.01990.19610.00990.00410.1657-0.00160.194593.9538138.4998215.1342
51.6070.8616-0.41171.9907-0.52261.5607-0.04290.1352-0.0696-0.13340.0454-0.07230.22040.11520.00210.17650.0684-0.01080.1626-0.01510.1698100.7344127.7674208.694
64.1425-2.9025-2.42962.85830.743.44850.08170.47460.0787-0.8475-0.00610.72720.0698-0.7473-0.10170.4479-0.0301-0.06930.35520.06290.438681.8548117.9649211.1037
75.54532.20392.0923.0398-1.4884.79710.06470.0971-0.8632-0.7144-0.3231-0.36080.5661-0.02560.19350.47270.06030.09110.19340.04570.388292.5783109.0147210.0023
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 686 )
6X-RAY DIFFRACTION6chain 'A' and (resid 687 through 712 )
7X-RAY DIFFRACTION7chain 'A' and (resid 713 through 736 )

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