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- PDB-6q2d: Crystal structure of Methanobrevibacter smithii Dph2 in complex w... -

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Basic information

Entry
Database: PDB / ID: 6q2d
TitleCrystal structure of Methanobrevibacter smithii Dph2 in complex with Methanobrevibacter smithii elongation factor 2
Components
  • 2-(3-amino-3-carboxypropyl)histidine synthase
  • Elongation factor 2EEF2
KeywordsTRANSFERASE / Radical / S-adenosylmethionine / enzyme / iron sulfur cluster
Function / homology
Function and homology information


2-(3-amino-3-carboxypropyl)histidine synthase / 2-(3-amino-3-carboxypropyl)histidine synthase activity / protein histidyl modification to diphthamide / translation elongation factor activity / 4 iron, 4 sulfur cluster binding / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Diphthamide synthesis DPH1/DPH2 / Diphthamide synthesis Dph2, archaea / Diphthamide synthesis DHP1/DPH2, eukaryotes and archaea / Diphthamide synthesis DPH1/DPH2, domain 1 / Diphthamide synthesis DPH1/DPH2, domain 2 / Diphthamide synthesis DPH1/DPH2, domain 3 / Putative diphthamide synthesis protein / Translation elongation factor EFG/EF2, archaeal / Elongation Factor G, domain II / Elongation Factor G, domain III ...Diphthamide synthesis DPH1/DPH2 / Diphthamide synthesis Dph2, archaea / Diphthamide synthesis DHP1/DPH2, eukaryotes and archaea / Diphthamide synthesis DPH1/DPH2, domain 1 / Diphthamide synthesis DPH1/DPH2, domain 2 / Diphthamide synthesis DPH1/DPH2, domain 3 / Putative diphthamide synthesis protein / Translation elongation factor EFG/EF2, archaeal / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Elongation factor 2 / 2-(3-amino-3-carboxypropyl)histidine synthase
Similarity search - Component
Biological speciesMethanobrevibacter smithii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsFenwick, M.K. / Dong, M. / Lin, H. / Ealick, S.E.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM124165 United States
CitationJournal: Biochemistry / Year: 2019
Title: The Crystal Structure of Dph2 in Complex with Elongation Factor 2 Reveals the Structural Basis for the First Step of Diphthamide Biosynthesis.
Authors: Fenwick, M.K. / Dong, M. / Lin, H. / Ealick, S.E.
History
DepositionAug 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: 2-(3-amino-3-carboxypropyl)histidine synthase
B: 2-(3-amino-3-carboxypropyl)histidine synthase
C: Elongation factor 2
F: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,5106
Polymers239,8064
Non-polymers7032
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.899, 322.979, 172.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 2-(3-amino-3-carboxypropyl)histidine synthase / Dph2


Mass: 38429.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanobrevibacter smithii (archaea) / Gene: Msm_1358 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A5UMY5, 2-(3-amino-3-carboxypropyl)histidine synthase
#2: Protein Elongation factor 2 / EEF2 / EF-2


Mass: 81473.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanobrevibacter smithii (archaea) / Gene: fusA, BK798_06620 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2H4U7K7
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
Has ligand of interestN

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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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: The reservoir solution contained 100 mM Tris, pH 7.2, 200 mM MgSO4, and 21 % (w/v) PEG400; NaCl was added to the reservoir to a final concentration of 300 mM after forming the drop

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.45→49.4 Å / Num. obs: 37395 / % possible obs: 99.7 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.7
Reflection shellResolution: 3.45→3.64 Å / Num. unique obs: 5369 / CC1/2: 0.568

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Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Methanobrevibacter smithii Dph2, Pyrococcus horikoshii EF-2 (5H7J)

5h7j


Resolution: 3.45→49.356 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.79
RfactorNum. reflection% reflection
Rfree0.2665 1864 5 %
Rwork0.2238 --
obs0.226 37270 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 522.52 Å2 / Biso mean: 208.7438 Å2 / Biso min: 82.69 Å2
Refinement stepCycle: final / Resolution: 3.45→49.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12169 0 16 0 12185
Biso mean--213.37 --
Num. residues----1680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.54330.44031220.462644X-RAY DIFFRACTION99
3.5433-3.64750.49131380.43382692X-RAY DIFFRACTION99
3.6475-3.76520.42691460.39272716X-RAY DIFFRACTION100
3.7652-3.89970.40851420.34982690X-RAY DIFFRACTION100
3.8997-4.05580.28481560.29832669X-RAY DIFFRACTION99
4.0558-4.24030.27211480.23932713X-RAY DIFFRACTION100
4.2403-4.46370.28171450.1922711X-RAY DIFFRACTION100
4.4637-4.74320.22591490.17462724X-RAY DIFFRACTION100
4.7432-5.1090.22831340.18072714X-RAY DIFFRACTION99
5.109-5.62250.24871480.19152727X-RAY DIFFRACTION99
5.6225-6.43460.26951400.21262756X-RAY DIFFRACTION100
6.4346-8.10110.22561290.20352803X-RAY DIFFRACTION100
8.1011-49.3560.24211670.19492847X-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)
14.9261-0.46252.30992.93031.66142.99190.2311-0.42810.29770.0220.0919-0.16750.11570.28610.00011.08060.0279-0.08370.7911-0.05651.087231.37427.232831.293
21.3412-0.58770.84850.7815-0.38470.36910.1515-0.5150.2925-0.1468-0.0634-0.5713-0.14370.6544-0.02691.22210.0339-0.02920.7498-0.04081.40979.833414.060614.2166
32.56881.2687-0.36522.18930.66341.3608-0.3048-0.27150.2133-0.22420.06350.24590.1288-0.3327-01.32230.09160.0191.1862-0.01221.3278-23.113824.530115.8941
43.0121-0.81510.43130.253-0.1940.8421-0.1865-1.20130.8460.23070.2631-0.2644-0.19120.52150.15761.32520.1633-0.07060.7113-0.14621.39965.81934.362926.5706
51.84020.93410.47460.51390.93367.0554-1.2865-0.14061.45430.9343-0.00542.153-2.3578-2.8319-0.02123.5288-0.46260.09541.9233-0.1883.696-39.609661.06385.0059
60.9150.4671-0.76990.54660.04621.1002-0.2681.08040.4261-1.08660.7911-0.3011-2.0579-1.03650.02822.87260.1156-0.40593.2308-0.38781.9515-12.01263.3096-7.0293
76.258-0.93376.78350.1622-1.02767.395-0.4935-2.23760.86971.9087-0.04371.2771-0.7216-2.5422-0.10052.2486-0.2110.06311.62910.16353.912-13.501152.0607-6.074
80.3375-0.4019-0.78535.1671-0.29682.61490.39020.9623-0.1630.0216-0.8017-2.51211.13490.4024-0.06162.1219-0.1976-0.5532.02720.12151.6682-29.721471.659122.72
90.40370.0520.1240.0083-0.0080.11740.1684-0.22821.25490.478-1.27660.3755-0.66590.501501.4038-0.00810.19632.0001-0.09771.4421-36.56273.9262-9.1461
101.94071.372-0.11140.925-0.1082-0.0129-0.79362.04860.4538-1.12420.17570.88630.0377-0.3602-0.07081.5069-0.3642-0.00821.401-0.28791.3651-29.836312.5524-14.0802
110.09680.0573-0.16170.86340.32380.37020.252-0.8677-0.1584-0.51660.9195-0.543-1.7104-0.593501.9979-0.30650.14712.6016-0.09281.8612-42.10414.31-11.9464
120.98660.94430.56621.70681.10240.6723-0.50270.428-0.0588-0.5060.12350.48760.8055-0.508701.66330.0571-0.0412.3843-0.0011.9979-57.241919.42552.6773
130.0146-0.02930.05320.68930.34230.5741-0.12520.63461.15190.2090.0977-0.5169-0.7238-0.087701.5580.193-0.00081.66750.17571.8831-51.590828.4743-0.0932
140.8388-0.6409-1.46770.44161.13012.2062-0.04190.4071-0.04750.12840.18260.5534-0.3584-1.159902.13020.2138-0.25512.00940.31352.1307-38.245943.0635-16.644
151.3419-0.0019-0.14420.0031-0.00210.0158-0.1445-3.2337-1.69590.5363-0.7621.0001-0.31151.3724-0.01511.94810.1141-0.2871.98440.35061.8579-39.613241.8953-10.2939
160.0107-0.0351-0.03050.04330.06240.0205-0.2802-0.95842.28010.81030.0980.8483-0.8294-0.8652-01.86220.20190.07792.07020.092.6153-51.544141.9024-13.293
173.76752.03290.15881.7042-0.18950.6633-0.30512.1371-0.4856-1.40570.3814-0.0531-0.06780.66850.00161.9993-0.1654-0.0392.24270.70761.537-16.376439.7346-31.5543
185.85235.48411.13598.96710.39990.30440.01913.33920.2931-0.0690.5781-1.5456-0.8544-2.11231.14031.755-0.06490.16113.18141.15291.91263.636938.4357-35.6578
190.12490.11090.13580.63510.24380.1105-0.20010.97610.7141-0.4858-0.3712-1.0944-0.21770.760701.7089-0.15150.19061.40610.17751.60523.2232.5269-24.7214
202.9431.2502-0.1281.46091.20431.5692-0.43540.6131-0.04140.10410.1340.312-0.23770.00301.39990.02530.12380.9771-0.15061.1275-8.717318.5016-12.9664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 3 through 342 )C3 - 342
2X-RAY DIFFRACTION2chain 'C' and (resid 343 through 465 )C343 - 465
3X-RAY DIFFRACTION3chain 'C' and (resid 466 through 619 )C466 - 619
4X-RAY DIFFRACTION4chain 'C' and (resid 620 through 730 )C620 - 730
5X-RAY DIFFRACTION5chain 'F' and (resid 388 through 476 )F388 - 476
6X-RAY DIFFRACTION6chain 'F' and (resid 477 through 539 )F477 - 539
7X-RAY DIFFRACTION7chain 'F' and (resid 540 through 619 )F540 - 619
8X-RAY DIFFRACTION8chain 'F' and (resid 620 through 715 )F620 - 715
9X-RAY DIFFRACTION9chain 'A' and (resid 1 through 18 )A1 - 18
10X-RAY DIFFRACTION10chain 'A' and (resid 19 through 78 )A19 - 78
11X-RAY DIFFRACTION11chain 'A' and (resid 79 through 102 )A79 - 102
12X-RAY DIFFRACTION12chain 'A' and (resid 103 through 157 )A103 - 157
13X-RAY DIFFRACTION13chain 'A' and (resid 158 through 208 )A158 - 208
14X-RAY DIFFRACTION14chain 'A' and (resid 209 through 290 )A209 - 290
15X-RAY DIFFRACTION15chain 'A' and (resid 291 through 313 )A291 - 313
16X-RAY DIFFRACTION16chain 'A' and (resid 314 through 329 )A314 - 329
17X-RAY DIFFRACTION17chain 'B' and (resid 5 through 124 )B5 - 124
18X-RAY DIFFRACTION18chain 'B' and (resid 125 through 157 )B125 - 157
19X-RAY DIFFRACTION19chain 'B' and (resid 158 through 203 )B158 - 203
20X-RAY DIFFRACTION20chain 'B' and (resid 204 through 329 )B204 - 329

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