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- PDB-3g27: Structure of a putative bacteriophage protein from Escherichia co... -

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Basic information

Entry
Database: PDB / ID: 3g27
TitleStructure of a putative bacteriophage protein from Escherichia coli str. K-12 substr. MG1655
Components82 prophage-derived uncharacterized protein ybcO
KeywordsPROTEIN BINDING / E.coli / prophage-associated / Zinc-binding / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


nuclease activity / Hydrolases; Acting on ester bonds / metal ion binding
Similarity search - Function
prophage-derive protein ybcO / Putative nuclease YbcO / Putative nuclease YbcO / Erythroid Transcription Factor GATA-1; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative nuclease YbcO
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsCuff, M.E. / Evdokimova, E. / Kudritska, M. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of a putative bacteriophage protein from Escherichia coli str. K-12 substr. MG1655
Authors: Cuff, M.E. / Evdokimova, E. / Kudritska, M. / Edwards, A. / Savchenko, A. / Joachimiak, A.
History
DepositionJan 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_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_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

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Assembly

Deposited unit
A: 82 prophage-derived uncharacterized protein ybcO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6254
Polymers10,4581
Non-polymers1683
Water79344
1
A: 82 prophage-derived uncharacterized protein ybcO
hetero molecules

A: 82 prophage-derived uncharacterized protein ybcO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2518
Polymers20,9162
Non-polymers3356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1370 Å2
ΔGint-23 kcal/mol
Surface area8210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.311, 71.311, 32.333
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 82 prophage-derived uncharacterized protein ybcO


Mass: 10457.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: predicted prophage protein / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 substr. MG1655 / Gene: b0549, JW0537, ybcO / Plasmid: modified p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P68661
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M CaCl2, 20%PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 24, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionRedundancy: 9.9 % / Av σ(I) over netI: 48.64 / Number: 59799 / Rmerge(I) obs: 0.065 / Χ2: 1.62 / D res high: 2.05 Å / D res low: 50 Å / Num. obs: 6049 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.055098.210.0574.2819.5
4.015.0599.310.0482.7459.9
3.514.0199.510.0491.9310.9
3.183.5110010.0581.63811.1
2.963.1810010.0741.56411.1
2.782.9610010.081.40111.4
2.642.7810010.111.25311.3
2.532.6410010.1191.1811.2
2.432.5310010.1231.07811.1
2.352.4310010.1721.09610.3
2.272.3510010.1851.1339.6
2.212.2799.710.1811.1358.8
2.152.2199.510.2461.0837.5
2.12.1595.310.1771.0347.7
2.052.187.710.2261.0696.1
ReflectionResolution: 2.05→50 Å / Num. all: 6049 / Num. obs: 6049 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.616 / Net I/σ(I): 48.638
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.226 / Num. unique all: 341 / Χ2: 1.069 / % possible all: 87.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementResolution: 2.1→30.88 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.26 / WRfactor Rwork: 0.202 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.873 / SU B: 8.773 / SU ML: 0.12 / SU R Cruickshank DPI: 0.207 / SU Rfree: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.185
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.249 260 4.6 %RANDOM
Rwork0.186 ---
all0.188 5697 --
obs0.188 5697 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.59 Å2 / Biso mean: 36.079 Å2 / Biso min: 21.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å21.11 Å20 Å2
2--2.22 Å20 Å2
3----3.34 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms597 0 6 44 647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021621
X-RAY DIFFRACTIONr_bond_other_d0.0020.02421
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.948841
X-RAY DIFFRACTIONr_angle_other_deg0.931019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.625581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40322.30826
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.8211597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.801157
X-RAY DIFFRACTIONr_chiral_restr0.0810.297
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021701
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02125
X-RAY DIFFRACTIONr_mcbond_it0.7951.5407
X-RAY DIFFRACTIONr_mcbond_other0.1421.5165
X-RAY DIFFRACTIONr_mcangle_it1.5012649
X-RAY DIFFRACTIONr_scbond_it2.2853214
X-RAY DIFFRACTIONr_scangle_it3.8044.5192
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 16 -
Rwork0.22 391 -
all-407 -
obs--95.32 %
Refinement TLS params.Method: refined / Origin x: 5.4003 Å / Origin y: 28.9214 Å / Origin z: 4.7353 Å
111213212223313233
T0.1704 Å20.0615 Å20.0533 Å2-0.1128 Å20.0098 Å2--0.0275 Å2
L3.1005 °2-0.9572 °2-0.6178 °2-4.7295 °20.8007 °2--3.5165 °2
S-0.1553 Å °0.1396 Å °-0.2245 Å °0.1838 Å °-0.0502 Å °0.0898 Å °0.5656 Å °0.2408 Å °0.2055 Å °

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