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- PDB-5erv: Ternary complex of GephE - ADP - Tungsten cluster -

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Basic information

Entry
Database: PDB / ID: 5erv
TitleTernary complex of GephE - ADP - Tungsten cluster
ComponentsGephyrin
KeywordsTRANSFERASE / Moco / Wco / tungsten cofactor / Tungsten cluster / Biosynthesis / ternary complex
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 / : / TUNGSTATE(VI)ION / Gephyrin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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 1.2Mar 14, 2018Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization

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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)48,28317
Polymers45,6521
Non-polymers2,63016
Water6,846380
1
A: Gephyrin
hetero molecules

A: Gephyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,56534
Polymers91,3052
Non-polymers5,26032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area13660 Å2
ΔGint-231 kcal/mol
Surface area33730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.661, 99.675, 113.237
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-815-

MPD

21A-1224-

HOH

31A-1233-

HOH

41A-1254-

HOH

51A-1263-

HOH

61A-1279-

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 344-762
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 , 8 types, 396 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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: W
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: WO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate, 0.02 M calcium chloride, 30 % MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.2148 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2148 Å / Relative weight: 1
ReflectionResolution: 1.8→74.82 Å / Num. obs: 46251 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 12.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 13.5 % / Rmerge(I) obs: 2.134 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
SHELXphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.8→65.826 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 2251 4.87 %
Rwork0.156 --
obs0.1583 46249 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→65.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3152 0 59 380 3591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123402
X-RAY DIFFRACTIONf_angle_d1.4044659
X-RAY DIFFRACTIONf_dihedral_angle_d14.1761334
X-RAY DIFFRACTIONf_chiral_restr0.105541
X-RAY DIFFRACTIONf_plane_restr0.008612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83910.32181380.24582713X-RAY DIFFRACTION100
1.8391-1.88190.26871500.21692722X-RAY DIFFRACTION100
1.8819-1.9290.26311350.19892710X-RAY DIFFRACTION100
1.929-1.98120.22771530.1832732X-RAY DIFFRACTION100
1.9812-2.03950.22351430.16632707X-RAY DIFFRACTION100
2.0395-2.10530.18191160.15412730X-RAY DIFFRACTION100
2.1053-2.18050.21491300.15092761X-RAY DIFFRACTION100
2.1805-2.26780.16961300.13752709X-RAY DIFFRACTION100
2.2678-2.37110.17011360.13472767X-RAY DIFFRACTION100
2.3711-2.49610.2051380.13592725X-RAY DIFFRACTION100
2.4961-2.65250.20491370.14642764X-RAY DIFFRACTION100
2.6525-2.85730.21841590.14722720X-RAY DIFFRACTION100
2.8573-3.14480.19841570.14762745X-RAY DIFFRACTION100
3.1448-3.59980.18281470.14562768X-RAY DIFFRACTION100
3.5998-4.53530.1691510.13012790X-RAY DIFFRACTION100
4.5353-65.86970.22291310.18042935X-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)
10.4391-0.0687-0.16890.2380.08080.13780.10070.1944-0.1785-0.0606-0.03610.10520.0436-0.18450.07360.0552-0.0888-0.02240.07830.01450.1572-18.52431.25754.9718
20.0353-0.096-0.0768-0.08690.0478-0.0210.17560.1676-0.1106-0.0977-0.2142-0.003-0.143-0.1591-0.01720.20270.10970.04950.2283-0.01830.15085.265831.5232-40.2623
30.3412-0.0583-0.09440.04480.08930.10810.04450.0182-0.0565-0.0774-0.0787-0.19470.0098-0.0225-0.00820.17640.05140.09630.1813-0.050.26796.544728.6604-40.126
40.2965-0.0409-0.05590.2118-0.13140.10910.0074-0.036-0.00660.0435-0.02590.0149-0.0465-0.011500.0635-0.01880.00710.0522-0.00150.0599-6.687239.63658.6365
50.19410.1262-0.060.18210.01580.1488-0.025-0.17730.0470.19460.0370.1274-0.0136-0.1916-0.02110.1054-0.01980.01880.14390.00770.133-19.850836.825219.4719
60.011-0.0251-0.00440.0145-0.0149-0.0052-0.0139-0.0215-0.04970.0708-0.01570.00080.0863-0.0723-0.00910.1522-0.0229-0.01990.08670.00180.1276-9.90124.32866.9897
70.0375-0.00870.0250.09580.0190.0169-0.1389-0.05170.03580.15440.10720.10350.24680.119500.27440.01530.00740.1668-0.00630.25690.196113.264512.7559
80.0063-0.01290.01590.0099-0.02270.027-0.0061-0.14320.12390.14010.0368-0.30440.1320.197700.2228-0.0058-0.01040.2265-0.04190.32755.390718.905212.0424
90.05620.00720.06330.00470.01670.0854-0.01430.0181-0.2230.18780.03140.03840.16070.0252-0.00850.263-0.01160.04170.0963-0.00050.287-5.24589.822813.8568
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 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 627 )
6X-RAY DIFFRACTION6chain 'A' and (resid 628 through 661 )
7X-RAY DIFFRACTION7chain 'A' and (resid 662 through 686 )
8X-RAY DIFFRACTION8chain 'A' and (resid 687 through 712 )
9X-RAY DIFFRACTION9chain 'A' and (resid 713 through 736 )

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