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- PDB-6q2e: Crystal structure of Methanobrevibacter smithii Dph2 bound to 5'-... -

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Basic information

Entry
Database: PDB / ID: 6q2e
TitleCrystal structure of Methanobrevibacter smithii Dph2 bound to 5'-methylthioadenosine
Components2-(3-amino-3-carboxypropyl)histidine synthase
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 / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Diphthamide synthesis DPH1/DPH2 domain 1 / Diphthamide synthesis DPH1/DPH2 domain 2 / Diphthamide synthesis DPH1/DPH2 domain 3 / 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 ...Diphthamide synthesis DPH1/DPH2 domain 1 / Diphthamide synthesis DPH1/DPH2 domain 2 / Diphthamide synthesis DPH1/DPH2 domain 3 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-DEOXY-5'-METHYLTHIOADENOSINE / IRON/SULFUR CLUSTER / 2-(3-amino-3-carboxypropyl)histidine synthase
Similarity search - Component
Biological speciesMethanobrevibacter smithii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.768 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1937
Polymers76,8592
Non-polymers1,3335
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-70 kcal/mol
Surface area27080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.082, 81.020, 130.972
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O3S
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM bistrispropane, pH 6.5, 16-17 % (w/v) PEG2000 monomethyl ether, 6 mM 5'-methylthioadenosine and 14 mM 2-aminobutyrate. After drops were formed by combining the sample and reservoir ...Details: 100 mM bistrispropane, pH 6.5, 16-17 % (w/v) PEG2000 monomethyl ether, 6 mM 5'-methylthioadenosine and 14 mM 2-aminobutyrate. After drops were formed by combining the sample and reservoir solutions, 300 mM NaCl was added to the reservoirs prior to sealing

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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: 1.768→131 Å / Num. obs: 64613 / % possible obs: 97.6 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Net I/σ(I): 19.3
Reflection shellResolution: 1.77→1.86 Å / Num. unique obs: 9037 / CC1/2: 0.8

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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: Candidatus methanoperedens nitroreducens Dph2 bound to S-adenosylhomocysteine (PDB entry 6BXO)

6bxo


Resolution: 1.768→68.902 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.32
RfactorNum. reflection% reflection
Rfree0.2193 3157 4.89 %
Rwork0.1804 --
obs0.1823 64546 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.45 Å2 / Biso mean: 43.4542 Å2 / Biso min: 20.66 Å2
Refinement stepCycle: final / Resolution: 1.768→68.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5144 0 57 565 5766
Biso mean--38.04 51.76 -
Num. residues----659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.768-1.79440.30621380.28522385X-RAY DIFFRACTION89
1.7944-1.82240.30381220.26452604X-RAY DIFFRACTION97
1.8224-1.85230.3471220.24842636X-RAY DIFFRACTION96
1.8523-1.88420.27181380.23912621X-RAY DIFFRACTION98
1.8842-1.91850.27561490.22992649X-RAY DIFFRACTION97
1.9185-1.95540.27671440.22642638X-RAY DIFFRACTION98
1.9554-1.99530.25041570.21862639X-RAY DIFFRACTION98
1.9953-2.03870.23081340.2092638X-RAY DIFFRACTION97
2.0387-2.08610.25871230.20812606X-RAY DIFFRACTION95
2.0861-2.13830.28391380.20582705X-RAY DIFFRACTION98
2.1383-2.19610.28221560.20142613X-RAY DIFFRACTION98
2.1961-2.26080.24611110.20972715X-RAY DIFFRACTION98
2.2608-2.33370.23491310.20482689X-RAY DIFFRACTION98
2.3337-2.41710.21961570.20482658X-RAY DIFFRACTION99
2.4171-2.51390.26121340.20552714X-RAY DIFFRACTION98
2.5139-2.62830.25251230.20442716X-RAY DIFFRACTION98
2.6283-2.76690.28081420.20442691X-RAY DIFFRACTION99
2.7669-2.94030.26221370.19892702X-RAY DIFFRACTION98
2.9403-3.16730.23491410.18422612X-RAY DIFFRACTION95
3.1673-3.4860.21471370.17392761X-RAY DIFFRACTION99
3.486-3.99040.17231350.14052762X-RAY DIFFRACTION99
3.9904-5.02730.15961360.13672801X-RAY DIFFRACTION99
5.0273-68.90.19461520.17112834X-RAY DIFFRACTION96
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)
16.0293-0.6690.55410.7651-0.16482.1727-0.04830.08670.1224-0.10830.02430.0217-0.114-0.08940.02910.2626-0.01470.02510.15970.01880.19266.000441.7543-7.7681
25.11320.6881.74073.19380.64999.119-0.11870.08650.307-0.0723-0.06030.17130.0323-0.40950.14030.24980.062-0.0110.2967-0.00940.2556-17.732845.1794-8.3781
34.6861-0.0814-0.24561.6047-0.06622.8492-0.1521-0.1209-0.16050.06720.06790.20870.1934-0.25040.05720.23210.02030.05640.1753-0.00890.2191-11.060843.261618.5607
45.4961-1.1130.72316.43140.25386.0422-0.0129-0.68850.13480.49160.0419-0.43350.06260.2718-0.02750.26510.0379-0.01930.4017-0.01850.23768.517145.212731.9041
54.0397-3.10880.97934.606-1.09861.19180.02290.09370.29470.2092-0.1598-0.1919-0.00190.08350.14490.2501-0.03750.0020.2823-0.03540.292923.138334.774534.7088
62.1444-0.8443-0.73541.871-1.15587.88210.06280.15920.07590.1097-0.1912-0.10390.0950.1840.07910.2303-0.0023-0.01190.2363-0.02560.326830.606925.700330.8166
72.3993-0.9031.73472.4829-0.48133.76920.15310.0309-0.17680.07430.0509-0.07630.40850.1205-0.18550.22530.02810.00770.1914-0.04830.241323.401426.21947.476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 113 )A0 - 113
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 208 )A114 - 208
3X-RAY DIFFRACTION3chain 'A' and (resid 209 through 329 )A209 - 329
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 62 )B2 - 62
5X-RAY DIFFRACTION5chain 'B' and (resid 63 through 140 )B63 - 140
6X-RAY DIFFRACTION6chain 'B' and (resid 141 through 207 )B141 - 207
7X-RAY DIFFRACTION7chain 'B' and (resid 208 through 330 )B208 - 330

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