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- PDB-2p5z: The E. coli c3393 protein is a component of the type VI secretion... -

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Basic information

Entry
Database: PDB / ID: 2p5z
TitleThe E. coli c3393 protein is a component of the type VI secretion system and exhibits structural similarity to T4 bacteriophage tail proteins gp27 and gp5
ComponentsType VI secretion system componentType VI secretion system
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


identical protein binding
Similarity search - Function
Black beetle virus capsid protein - #10 / Black beetle virus capsid protein / Pnp Oxidase; Chain A - #50 / Gp5 N-terminal domain / Baseplate protein-like domains / Type VI secretion system spike protein VgrG2, C-terminal domain of unknown function DUF2345 / Putative type VI secretion system, Rhs element associated Vgr domain / Uncharacterized protein conserved in bacteria (DUF2345) / Putative type VI secretion system Rhs element Vgr / Type VI secretion system, RhsGE-associated Vgr family subset ...Black beetle virus capsid protein - #10 / Black beetle virus capsid protein / Pnp Oxidase; Chain A - #50 / Gp5 N-terminal domain / Baseplate protein-like domains / Type VI secretion system spike protein VgrG2, C-terminal domain of unknown function DUF2345 / Putative type VI secretion system, Rhs element associated Vgr domain / Uncharacterized protein conserved in bacteria (DUF2345) / Putative type VI secretion system Rhs element Vgr / Type VI secretion system, RhsGE-associated Vgr family subset / Phage tail baseplate hub (GPD) / Phage tail protein beta-alpha-beta fold / Type VI secretion system, RhsGE-associated Vgr protein / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / 3-Layer(bab) Sandwich / Pnp Oxidase; Chain A / Few Secondary Structures / Irregular / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesEscherichia coli O6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsRamagopal, U.A. / Bonanno, J.B. / Sridhar, V. / Lau, C. / Toro, R. / Gheyi, T. / Maletic, M. / Freeman, J.C. / Sauder, J.M. / Burley, S.K. ...Ramagopal, U.A. / Bonanno, J.B. / Sridhar, V. / Lau, C. / Toro, R. / Gheyi, T. / Maletic, M. / Freeman, J.C. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2009
Title: Type VI secretion apparatus and phage tail-associated protein complexes share a common evolutionary origin.
Authors: Leiman, P.G. / Basler, M. / Ramagopal, U.A. / Bonanno, J.B. / Sauder, J.M. / Pukatzki, S. / Burley, S.K. / Almo, S.C. / Mekalanos, J.J.
History
DepositionMar 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Type VI secretion system component


Theoretical massNumber of molelcules
Total (without water)55,6981
Polymers55,6981
Non-polymers00
Water1,11762
1
X: Type VI secretion system component

X: Type VI secretion system component

X: Type VI secretion system component


Theoretical massNumber of molelcules
Total (without water)167,0943
Polymers167,0943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area4440 Å2
ΔGint-21 kcal/mol
Surface area50070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.351, 116.351, 80.584
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
DetailsBiological unit appears to be trimer

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Components

#1: Protein Type VI secretion system component / Type VI secretion system


Mass: 55697.988 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6 (bacteria) / Species: Escherichia coli / Strain: O6:H1, CFT073, UPEC / Gene: c3393 / Plasmid: BC-pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8FED2, UniProt: A0A0H2VBP9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Hepes pH 7.5, 21% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 19128 / Num. obs: 19128 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.5 % / Rmerge(I) obs: 0.107 / Rsym value: 0.095 / Χ2: 1.442 / Net I/σ(I): 6.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1892 / Rsym value: 0.558 / Χ2: 0.427 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
HKL-2000data reduction
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.6→47.19 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.926 / SU B: 10.191 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.395 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 983 5.1 %RANDOM
Rwork0.217 ---
all0.219 19100 --
obs0.219 19100 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.297 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20.78 Å20 Å2
2--1.57 Å20 Å2
3----2.35 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2891 0 0 62 2953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222959
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.9624001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5155356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55322.69145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.27115502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1541531
X-RAY DIFFRACTIONr_chiral_restr0.1410.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022259
X-RAY DIFFRACTIONr_nbd_refined0.160.11203
X-RAY DIFFRACTIONr_nbtor_refined0.3220.31957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.5203
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1110.138
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.57
X-RAY DIFFRACTIONr_mcbond_it2.89621832
X-RAY DIFFRACTIONr_mcangle_it4.63432894
X-RAY DIFFRACTIONr_scbond_it3.10521263
X-RAY DIFFRACTIONr_scangle_it4.65831107
LS refinement shellResolution: 2.6→2.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 89 -
Rwork0.318 1321 -
obs-1410 99.86 %

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