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- PDB-4ax2: New Type VI-secreted toxins and self-resistance proteins in Serra... -

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Basic information

Entry
Database: PDB / ID: 4ax2
TitleNew Type VI-secreted toxins and self-resistance proteins in Serratia marcescens
ComponentsRAP1B
KeywordsTOXIN / RESISTANCE PROTEIN / HELICAL FOLD / S-SAD PHASING
Function / homologyType VI secretion system (T6SS), amidase immunity protein / T6SS superfamily / Type VI secretion system (T6SS), amidase immunity protein / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1620 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / IODIDE ION / Rap1b
Function and homology information
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.88 Å
AuthorsEnglish, G. / Trunk, K. / Rao, V.A. / Srikannathasan, V. / Fritsch, M.J. / Guo, M. / Hunter, W.N. / Coulthurst, S.J.
CitationJournal: Mol.Microbiol. / Year: 2012
Title: New Secreted Toxins and Immunity Proteins Encoded within the Type Vi Secretion System Gene Cluster of Serratia Marcescens
Authors: English, G. / Trunk, K. / Rao, V.A. / Srikannathasan, V. / Hunter, W.N. / Coulthurst, S.J.
History
DepositionJun 7, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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: RAP1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9298
Polymers16,3641
Non-polymers5647
Water2,000111
1
A: RAP1B
hetero molecules

A: RAP1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,85716
Polymers32,7292
Non-polymers1,12814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area5260 Å2
ΔGint-31.3 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.970, 77.970, 50.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RAP1B


Mass: 16364.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Strain: DB10 / Plasmid: PET15BTEV_PSC503 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA-GAMI (DE3) / References: UniProt: K4DIE5*PLUS
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsIODIDE ION (IOD): HALIDE SOAK. IODIDES USED FOR SAD PHASING ALONG WITH S ATOMS.
Sequence detailsGENOME IS NOT YET IN ANY DATABASE

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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: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.55M LI2SO4, 5% PEG 8000, pH 7.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Mar 24, 2011 / Details: MIRRORS
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→67.5 Å / Num. obs: 14813 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.6
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.88→67.52 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.609 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21898 748 5.1 %RANDOM
Rwork0.18002 ---
obs0.18187 14043 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0.7 Å20 Å2
2---1.39 Å20 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 1.88→67.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms993 0 22 111 1126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021091
X-RAY DIFFRACTIONr_bond_other_d0.0010.02795
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.961462
X-RAY DIFFRACTIONr_angle_other_deg0.8883.0061917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1125124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47625.34558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05915218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.066157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211154
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02197
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.877→1.926 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 54 -
Rwork0.268 940 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -13.0715 Å / Origin y: 38.0344 Å / Origin z: 9.0678 Å
111213212223313233
T0.007 Å2-0.0172 Å2-0.0001 Å2-0.0486 Å2-0.0149 Å2--0.0682 Å2
L1.3468 °20.578 °2-0.1574 °2-1.6878 °2-0.5675 °2--1.5682 °2
S0.0188 Å °-0.0764 Å °-0.0304 Å °-0.033 Å °0.0734 Å °-0.0582 Å °-0.0358 Å °0.077 Å °-0.0921 Å °

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