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- PDB-2v9v: Crystal Structure of Moorella thermoacetica SelB(377-511) -

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Basic information

Entry
Database: PDB / ID: 2v9v
TitleCrystal Structure of Moorella thermoacetica SelB(377-511)
ComponentsSELENOCYSTEINE-SPECIFIC ELONGATION FACTOR
KeywordsTRANSCRIPTION / PROTEIN CONFORMATIONAL CHANGE / TRANSCRIPTION ELONGATION FACTOR SELB / SELENOPROTEIN BIOSYNTHESIS / PROTEIN DYNAMICS / NUCLEOTIDE-BINDING / CYTOPLASM / GTP-BINDING / SELENOCYSTEINE / WINGED-HELIX DOMAIN / PROTEIN BIOSYNTHESIS
Function / homology
Function and homology information


selenocysteine incorporation / translation elongation factor activity / GTPase activity / GTP binding / RNA binding / cytoplasm
Similarity search - Function
Translation elongation factor SelB, winged helix, type 1 / Elongation factor SelB, winged helix / Translation elongation factor SelB, winged helix, type 2 / Elongation factor SelB, winged helix / Translation elongation factor SelB, winged helix, type 3 / Elongation factor SelB, winged helix / Translation elongation factor, selenocysteine-specific / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translational (tr)-type guanine nucleotide-binding (G) domain signature. ...Translation elongation factor SelB, winged helix, type 1 / Elongation factor SelB, winged helix / Translation elongation factor SelB, winged helix, type 2 / Elongation factor SelB, winged helix / Translation elongation factor SelB, winged helix, type 3 / Elongation factor SelB, winged helix / Translation elongation factor, selenocysteine-specific / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 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. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Small GTP-binding protein domain / Arc Repressor Mutant, subunit A / Translation protein, beta-barrel domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Selenocysteine-specific elongation factor
Similarity search - Component
Biological speciesMOORELLA THERMOACETICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsGanichkin, O. / Wahl, M.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Conformational Switches in Winged-Helix Domains 1 and 2 of Bacterial Translation Elongation Factor Selb.
Authors: Ganichkin, O. / Wahl, M.C.
History
DepositionAug 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SELENOCYSTEINE-SPECIFIC ELONGATION FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7117
Polymers15,5231
Non-polymers1886
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.349, 46.087, 58.683
Angle α, β, γ (deg.)90.00, 120.45, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2016-

HOH

21A-2039-

HOH

31A-2040-

HOH

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Components

#1: Protein SELENOCYSTEINE-SPECIFIC ELONGATION FACTOR / SELB / SELB TRANSLATION FACTOR


Mass: 15523.494 Da / Num. of mol.: 1 / Fragment: WINGED-HELIX DOMAINS 1 AND 2, RESIDUES 377-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MOORELLA THERMOACETICA (bacteria) / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2 (DE3) / References: UniProt: Q46455
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 1.65 Å3/Da / Density % sol: 49.86 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100 MM HEPES-NAOH, PH 6.9 TO 7.9, 3.9 TO 4.5 M NACL, HANGING DROP VAPOR DIFFUSION AT 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.8
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. obs: 61009 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RESIDUES 377-511 OF PDB ENTRY 1LVA

1lva


Resolution: 1.1→20 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.669 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.141 3094 5.1 %RANDOM
Rwork0.12 ---
obs0.121 57911 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20.08 Å2
2---0.43 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 6 318 1421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211245
X-RAY DIFFRACTIONr_bond_other_d0.0020.021179
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9491704
X-RAY DIFFRACTIONr_angle_other_deg0.8832695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.4495159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.822.42466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.02515212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3871517
X-RAY DIFFRACTIONr_chiral_restr0.0930.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021494
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02323
X-RAY DIFFRACTIONr_nbd_refined0.2350.2288
X-RAY DIFFRACTIONr_nbd_other0.1950.21230
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2630
X-RAY DIFFRACTIONr_nbtor_other0.0880.2684
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.2202
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3290.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.255
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.41.5753
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06621216
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9553512
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1484.5487
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.13 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.182 220
Rwork0.155 4291

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