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- PDB-3mfb: Crystal Structure of the S-type Pyocin domain of ECA1669 protein ... -

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Basic information

Entry
Database: PDB / ID: 3mfb
TitleCrystal Structure of the S-type Pyocin domain of ECA1669 protein from Erwinia carotovora, Northeast Structural Genomics Consortium Target EwR82C
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyS-type Pyocin / PAAR motif / PAAR motif / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / killing of cells of another organism / defense response to bacterium / Pyosin/cloacin translocation domain-containing protein
Function and homology information
Biological speciesErwinia carotovora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target EwR82C
Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionApr 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)73,2354
Polymers73,2354
Non-polymers00
Water5,999333
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)18,3091
Polymers18,3091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)18,3091
Polymers18,3091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)18,3091
Polymers18,3091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)18,3091
Polymers18,3091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.076, 52.307, 62.161
Angle α, β, γ (deg.)69.500, 90.040, 90.040
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Uncharacterized protein


Mass: 18308.777 Da / Num. of mol.: 4 / Fragment: S-type Pyocin domain residues 332-479
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia carotovora (bacteria) / Strain: SCRI1043 / Gene: ECA1669 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q6D6L3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.1M MES (pH 6.5), 30% PEG 5K MME, and 0.2M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97885 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 25, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 60424 / Num. obs: 56618 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 7.5 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.046 / Net I/σ(I): 15.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 7.3 / Num. unique all: 6084 / Rsym value: 0.121 / % possible all: 83.9

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Processing

Software
NameVersionClassificationNB
CNS1.2 & XtalViewrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→19.41 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000944.188 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2556 4.9 %RANDOM
Rwork0.232 ---
all0.236 59924 --
obs0.234 52254 87.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.021 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.29 Å2-0.66 Å20.14 Å2
2---5.09 Å2-4.44 Å2
3---10.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4820 0 0 333 5153
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.39 185 4.7 %
Rwork0.391 3775 -
obs-3960 65.5 %

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