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- PDB-3zfi: Rap1a protein (SMA2260) from Serratia marcescens -

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Basic information

Entry
Database: PDB / ID: 3zfi
TitleRap1a protein (SMA2260) from Serratia marcescens
ComponentsRAP1A PROTEIN
KeywordsTRANSPORT PROTEIN / BACTERIAL IMMUNITY / 2260 PROTEIN / T6SS / TYPE VI SECRETION SYSTEM / SELF-RESISTANCE PROTEIN
Function / homology10k-s Protein, Hypothetical Protein A; Chain A - #40 / Rap1a immunity protein / Rap1a immunity proteins / 10k-s Protein, Hypothetical Protein A; Chain A / Orthogonal Bundle / Mainly Alpha / Rap1a protein
Function and homology information
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsSrikannathasan, V. / O'Rourke, P.E.F. / Rao, V.A. / English, G. / Coulthurst, S.J. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural Basis for Type Vi Secreted Peptidoglycan Dl-Endopeptidase Function, Specificity and Neutralization in Serratia Marcescens
Authors: Srikannathasan, V. / English, G. / Bui, N.K. / Trunk, K. / Rourke, P.E.F.O. / Rao, V.A. / Vollmer, W. / Coulthurst, S.J. / Hunter, W.N.
History
DepositionDec 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Nov 6, 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: RAP1A PROTEIN
B: RAP1A PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,6552
Polymers23,6552
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-12.4 kcal/mol
Surface area9140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.650, 93.000, 51.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein RAP1A PROTEIN


Mass: 11827.369 Da / Num. of mol.: 2 / Fragment: MATURE PROTEIN (SIGNAL PEPTIDE CLEAVED)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Strain: DB10 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: S4S1V8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.26 Å3/Da / Density % sol: 45.53 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.5
Details: SITTING DROP VAPOUR DIFFUSION. PROTEIN CONCENTRATION AT 9MG/ML, IN 150 MM SODIUM CHLORIDE, 25MM TRIS-HCL, PH 7.5 (SAMPLE BUFFER) RESERVOIR: 25% W/V POLYETHYLENE GLYCOL 3350, 0.1M BIS-TRIS, ...Details: SITTING DROP VAPOUR DIFFUSION. PROTEIN CONCENTRATION AT 9MG/ML, IN 150 MM SODIUM CHLORIDE, 25MM TRIS-HCL, PH 7.5 (SAMPLE BUFFER) RESERVOIR: 25% W/V POLYETHYLENE GLYCOL 3350, 0.1M BIS-TRIS, PH 5.5 2:1 SAMPLE TO RESERVOIR RATIO.

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2011 / Details: COMPOUND REFRACTIVE LENSES
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.98→46.5 Å / Num. obs: 14089 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.4
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALACCP4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→61.78 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.28 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23396 706 5 %RANDOM
Rwork0.19216 ---
obs0.19416 13371 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.714 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.53 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.98→61.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 0 57 1565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021555
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.9552102
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5745185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.97623.33381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00915267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6651513
X-RAY DIFFRACTIONr_chiral_restr0.120.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211197
X-RAY DIFFRACTIONr_gen_planes_other
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: 1.981→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 50 -
Rwork0.25 893 -
obs--99.89 %

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