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- PDB-3wtr: Crystal structure of E. coli YfcM bound to Co(II) -

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Basic information

Entry
Database: PDB / ID: 3wtr
TitleCrystal structure of E. coli YfcM bound to Co(II)
ComponentsUncharacterized protein
KeywordsTRANSLATION / Hydroxylation
Function / homologyElongation factor P hydroxylase / Elongation factor P hydroxylase / metal ion binding / : / Elongation factor P hydroxylase / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsKobayashi, K. / Ishii, R. / Ishitani, R. / Nureki, O.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: The non-canonical hydroxylase structure of YfcM reveals a metal ion-coordination motif required for EF-P hydroxylation
Authors: Kobayashi, K. / Katz, A. / Rajkovic, A. / Ishii, R. / Branson, O.E. / Freitas, M.A. / Ishitani, R. / Ibba, M. / Nureki, O.
History
DepositionApr 19, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2792
Polymers22,2201
Non-polymers591
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.289, 36.938, 37.544
Angle α, β, γ (deg.)90.00, 101.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 22219.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: KTE5 / Gene: WCE_02429 / Production host: Escherichia coli (E. coli) / References: UniProt: L2V0E0, UniProt: A0A0J9X1Z5*PLUS
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.9 Å3/Da / Density % sol: 35.33 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 26% PEG 3350, 180mM ammonium sulfate, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.6049 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 1, 2013
RadiationMonochromator: Rotated-inclined double-crystal monochromator, Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6049 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 12114 / Biso Wilson estimate: 21.77 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PDN

4pdn


Resolution: 1.96→36.82 Å / FOM work R set: 0.8873 / SU ML: 0.15 / σ(F): 1.56 / Phase error: 18.75 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2067 581 5.02 %
Rwork0.17 --
obs0.1718 11581 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.15 Å2 / Biso mean: 24.44 Å2 / Biso min: 11.04 Å2
Refinement stepCycle: LAST / Resolution: 1.96→36.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1128 0 1 73 1202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081166
X-RAY DIFFRACTIONf_angle_d0.9821595
X-RAY DIFFRACTIONf_chiral_restr0.045168
X-RAY DIFFRACTIONf_plane_restr0.006208
X-RAY DIFFRACTIONf_dihedral_angle_d14.134397
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9596-2.04880.21481390.16712626276595
2.0488-2.15680.221430.16832730287397
2.1568-2.29190.19561460.16712759290598
2.2919-2.46880.2151430.17142759290299
2.4688-2.71720.20391510.17622749290099
2.7172-3.11020.19521480.17552819296799
3.1102-3.91780.22491460.170327412887100
3.9178-36.82630.19561460.16628172963100

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