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- PDB-6u45: Crystal structure of Methanoperedens nitroreducens elongation fac... -

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Basic information

Entry
Database: PDB / ID: 6u45
TitleCrystal structure of Methanoperedens nitroreducens elongation factor 2 bound to GMPPCP and magnesium
ComponentsElongation factor 2EEF2
KeywordsTRANSLATION / GTPase / ribosomal translocase / elongation
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
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 ...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
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Elongation factor 2
Similarity search - Component
Biological speciesCandidatus Methanoperedens nitroreducens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsFenwick, M.K. / Ealick, S.E.
CitationJournal: Curr Res Struct Biol / Year: 2020
Title: Structural basis of elongation factor 2 switching
Authors: Fenwick, M.K. / Ealick, S.E.
History
DepositionAug 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor 2
B: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,8438
Polymers161,6812
Non-polymers1,1626
Water10,449580
1
A: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4224
Polymers80,8411
Non-polymers5813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Elongation factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4224
Polymers80,8411
Non-polymers5813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.699, 134.375, 150.485
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 Elongation factor 2 / EEF2 / EF-2


Mass: 80840.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Methanoperedens nitroreducens (archaea)
Gene: fusA, ANME2D_00299 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A062V290
#2: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 3 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES or imidazole, pH 8.3, 200 mM sodium malonate, 16-18 % (w/v) PEG4000, 9 mM GppCp, and 15 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.35→150.5 Å / Num. obs: 79562 / % possible obs: 99.5 % / Redundancy: 10.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Net I/σ(I): 15
Reflection shellResolution: 2.35→2.4 Å / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4201 / CC1/2: 0.715

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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: Methanoperedens nitroreducens elongation factor 2 H595N (triclinic crystal form)

Resolution: 2.35→100.231 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.26
RfactorNum. reflection% reflection
Rfree0.2244 3993 5.03 %
Rwork0.1684 --
obs0.1713 79362 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 175.84 Å2 / Biso mean: 71.3992 Å2 / Biso min: 30.38 Å2
Refinement stepCycle: final / Resolution: 2.35→100.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10917 0 68 580 11565
Biso mean--51.94 71.11 -
Num. residues----1429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.37770.42121190.37382415X-RAY DIFFRACTION93
2.3777-2.40670.35061480.31572505X-RAY DIFFRACTION97
2.4067-2.43710.3691440.27562546X-RAY DIFFRACTION99
2.4371-2.46920.33181360.26522562X-RAY DIFFRACTION100
2.4692-2.5030.30071370.24782582X-RAY DIFFRACTION100
2.503-2.53880.2781360.23552570X-RAY DIFFRACTION99
2.5388-2.57670.32011370.22672552X-RAY DIFFRACTION100
2.5767-2.6170.31861490.23512596X-RAY DIFFRACTION100
2.617-2.65990.3351300.23042564X-RAY DIFFRACTION100
2.6599-2.70570.32031220.22292599X-RAY DIFFRACTION100
2.7057-2.75490.30941230.22392609X-RAY DIFFRACTION100
2.7549-2.80790.29641300.22982593X-RAY DIFFRACTION100
2.8079-2.86530.29961440.2172570X-RAY DIFFRACTION100
2.8653-2.92760.26861300.2152635X-RAY DIFFRACTION100
2.9276-2.99570.27541220.20922585X-RAY DIFFRACTION100
2.9957-3.07060.29071370.21642581X-RAY DIFFRACTION100
3.0706-3.15360.30531460.21472602X-RAY DIFFRACTION100
3.1536-3.24640.24661240.1962614X-RAY DIFFRACTION100
3.2464-3.35120.27741440.19692615X-RAY DIFFRACTION100
3.3512-3.4710.23891320.18252613X-RAY DIFFRACTION100
3.471-3.610.22771450.17892587X-RAY DIFFRACTION100
3.61-3.77430.2361430.16432611X-RAY DIFFRACTION100
3.7743-3.97330.24651310.15262626X-RAY DIFFRACTION100
3.9733-4.22220.18651360.13492634X-RAY DIFFRACTION100
4.2222-4.54820.16861500.12062615X-RAY DIFFRACTION100
4.5482-5.00590.18161230.11122673X-RAY DIFFRACTION100
5.0059-5.73020.16871520.12912643X-RAY DIFFRACTION100
5.7302-7.21920.20661640.15792676X-RAY DIFFRACTION100
7.2192-100.2310.16761590.14662796X-RAY DIFFRACTION99
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)
11.77360.2235-0.35751.2115-0.28992.4758-0.07340.0756-0.0592-0.00460.02790.150.2324-0.1760.05070.4260.06010.02080.4237-0.04710.43543.15966.18766.7154
21.6767-0.2966-0.59332.39350.93522.5989-0.1489-0.0756-0.3878-0.22910.0111-0.23240.30230.31140.17780.38320.0690.06990.39160.04060.498741.2099-29.63323.1164
31.77830.00770.9931.61790.59984.7068-0.05620.2785-0.0675-0.17240.0452-0.0447-0.55840.28030.02680.39250.0443-0.03050.39060.02280.383833.9703-3.94966.9414
43.7824-0.5784-0.03463.0965-0.19793.859-0.1225-0.74280.41460.32120.1069-0.1461-0.56830.29830.01520.66040.06030.04550.5711-0.11910.43476.43731.462333.4117
52.79340.567-0.68372.8401-0.26382.68650.10480.29370.4722-0.2896-0.05350.0688-0.8331-0.3373-0.03820.74680.140.08510.4670.02510.4804-3.624733.93539.7467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 400 through 728 )A400 - 728
2X-RAY DIFFRACTION2chain 'B' and (resid 4 through 450 )B4 - 450
3X-RAY DIFFRACTION3chain 'B' and (resid 451 through 728 )B451 - 728
4X-RAY DIFFRACTION4chain 'A' and (resid 3 through 254 )A3 - 254
5X-RAY DIFFRACTION5chain 'A' and (resid 255 through 399 )A255 - 399

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