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- PDB-5cof: Crystal structure of Uncharacterised protein Q1R1X2 from Escheric... -

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Basic information

Entry
Database: PDB / ID: 5cof
TitleCrystal structure of Uncharacterised protein Q1R1X2 from Escherichia coli UTI89
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Bacteriocin / sporulation / DUF1706 / cell cycle
Function / homologyProtein of unknown function DUF1706 / Protein of unknown function (DUF1706) / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / metal ion binding / Mainly Alpha / ClbS/DfsB family four-helix bundle protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsTaylor, J.D. / Hare, S. / Matthews, S.J.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structures of the DfsB Protein Family Suggest a Cationic, Helical Sibling Lethal Factor Peptide.
Authors: Taylor, J.D. / Taylor, G. / Hare, S.A. / Matthews, S.J.
History
DepositionJul 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1896
Polymers19,9321
Non-polymers2575
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-54 kcal/mol
Surface area9090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.860, 48.160, 80.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized protein


Mass: 19931.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain UTI89 / UPEC) (bacteria)
Strain: UTI89 / UPEC / Gene: UTI89_P066 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1R1X2

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Non-polymers , 5 types, 359 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 60 mM Magnesium chloride hexahydrate, 60 mM Calcium chloride dihydrate, 0.1 M imidazole, 0.1 M MES monohydrate, pH 6.5, 12.5% MPD, 12.5 % PEG 1000, 12.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.26→41.34 Å / Num. obs: 38126 / % possible obs: 98.93 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 13
Reflection shellResolution: 1.35→1.385 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.5 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PHENIXphasing
xia2data scaling
xia2data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.35→41.29 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.246 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13846 2073 5.2 %RANDOM
Rwork0.11511 ---
obs0.11632 38126 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.489 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.35→41.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 12 354 1744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021524
X-RAY DIFFRACTIONr_bond_other_d0.0070.021482
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9842099
X-RAY DIFFRACTIONr_angle_other_deg0.97233426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3195205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54225.07567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.98415257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.378156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021727
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02341
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8330.766723
X-RAY DIFFRACTIONr_mcbond_other0.7980.762722
X-RAY DIFFRACTIONr_mcangle_it1.151.151911
X-RAY DIFFRACTIONr_mcangle_other1.1571.156912
X-RAY DIFFRACTIONr_scbond_it1.1251.011801
X-RAY DIFFRACTIONr_scbond_other1.1251.014802
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4311.431171
X-RAY DIFFRACTIONr_long_range_B_refined3.6189.8222276
X-RAY DIFFRACTIONr_long_range_B_other2.0537.5061971
X-RAY DIFFRACTIONr_rigid_bond_restr4.53733006
X-RAY DIFFRACTIONr_sphericity_free32.217543
X-RAY DIFFRACTIONr_sphericity_bonded8.59353270
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 136 -
Rwork0.152 2502 -
obs--89.36 %

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