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- PDB-4b6i: Crystal structure Rap2b (SMA2266) from Serratia marcescens -

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Basic information

Entry
Database: PDB / ID: 4b6i
TitleCrystal structure Rap2b (SMA2266) from Serratia marcescens
ComponentsSMA2266
KeywordsSIGNALING PROTEIN
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 / Sma2266
Function and homology information
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.95 Å
AuthorsSrikannathasan, V. / Hunter, W.N.
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
DepositionAug 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Jul 17, 2013Group: Database references
Revision 1.4Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMA2266
B: SMA2266
C: SMA2266
D: SMA2266


Theoretical massNumber of molelcules
Total (without water)45,8984
Polymers45,8984
Non-polymers00
Water2,882160
1
A: SMA2266
D: SMA2266


Theoretical massNumber of molelcules
Total (without water)22,9492
Polymers22,9492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-16.1 kcal/mol
Surface area10100 Å2
MethodPISA
2
B: SMA2266
C: SMA2266


Theoretical massNumber of molelcules
Total (without water)22,9492
Polymers22,9492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-15.7 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.055, 56.894, 122.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11D-2006-

HOH

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Components

#1: Protein
SMA2266


Mass: 11474.593 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: J9PBR6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.77 % / Description: NONE
Crystal growpH: 4 / Details: 1 M LICL2, 20% PEG 6K, 0.1 M CITRIC ACID PH 4.0

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Dec 19, 2011
RadiationMonochromator: CU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→44.78 Å / Num. obs: 23682 / % possible obs: 10 % / Redundancy: 6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 2→44.78 Å / Redundancy: 6 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 11.5 / % possible all: 100

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Processing

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

Resolution: 1.95→61.1 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.301 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22873 1269 5.1 %RANDOM
Rwork0.17558 ---
obs0.17824 23682 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.955 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2---0.64 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.95→61.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 0 160 3344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023263
X-RAY DIFFRACTIONr_bond_other_d0.0010.022218
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.954391
X-RAY DIFFRACTIONr_angle_other_deg1.0533.0035411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4375406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.13525.595168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.80315601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1561516
X-RAY DIFFRACTIONr_chiral_restr0.1150.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02642
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 79 -
Rwork0.19 1388 -
obs--87.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2211-1.027-0.36861.70760.25851.3593-0.0122-0.05220.00720.04350.0739-0.02610.1240.1599-0.06170.01230.0157-0.00560.055-0.01330.021635.788849.197911.444
21.3727-0.4490.71632.0856-0.36852.21370.05170.035-0.132-0.09410.00710.08870.25190.0808-0.05880.04350.0137-0.01780.0058-0.00820.02697.409216.624619.0653
30.9593-0.05380.01242.12760.15521.07160.08880.0386-0.0155-0.1985-0.06590.15640.0141-0.0316-0.02290.02810.0136-0.01580.0241-0.00160.01314.321832.522214.6894
41.54230.11730.07461.28670.17261.4159-0.0214-0.10840.1159-0.0129-0.01930.02710.03310.02530.04070.02020.00690.01740.021-0.00780.029420.389554.21416.0695
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 119
2X-RAY DIFFRACTION2B20 - 119
3X-RAY DIFFRACTION3C18 - 119
4X-RAY DIFFRACTION4D18 - 119

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