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- PDB-3zib: Rap2a protein (SMA2265) from Serratia marcescens -

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Basic information

Entry
Database: PDB / ID: 3zib
TitleRap2a protein (SMA2265) from Serratia marcescens
ComponentsRAP2A SMA2265
KeywordsPROTEIN BINDING / IMMUNE SYSTEM / TYPE VI SECRETION / BACTERIAL IMMUNITY PROTEIN
Function / homologyFour Helix Bundle (Hemerythrin (Met), subunit A) - #1620 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionJan 8, 2013Deposition 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 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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: RAP2A SMA2265
B: RAP2A SMA2265
C: RAP2A SMA2265
D: RAP2A SMA2265


Theoretical massNumber of molelcules
Total (without water)45,7874
Polymers45,7874
Non-polymers00
Water2,468137
1
A: RAP2A SMA2265
B: RAP2A SMA2265


Theoretical massNumber of molelcules
Total (without water)22,8942
Polymers22,8942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-14.5 kcal/mol
Surface area9260 Å2
MethodPISA
2
C: RAP2A SMA2265
D: RAP2A SMA2265


Theoretical massNumber of molelcules
Total (without water)22,8942
Polymers22,8942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-14.6 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.650, 81.350, 58.450
Angle α, β, γ (deg.)90.00, 91.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RAP2A SMA2265


Mass: 11446.870 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Strain: DB10 / Production host: ESCHERICHIA COLI (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.06 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: SITTING DROP VAPOUR DIFFUSION. PROTEIN BUFFER: 10 MM SODIUM PHOSPHATE, PH 6.4 RESERVOIR CONDITION: 25% W/V POLYETHYLENE GLYCOL 1000, 0.1 M MES, PH6.5. CRYOPROTECTANT USED: 20% GLYCEROL WITH MOTHER LIQUOR.

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.96112
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2012 / Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR
RadiationMonochromator: DOUBLE CRYSTAL SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96112 Å / Relative weight: 1
ReflectionResolution: 1.9→40.6 Å / Num. obs: 29067 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALACCP4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B6I

4b6i


Resolution: 1.9→58.43 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.24 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23358 1477 5.1 %RANDOM
Rwork0.18306 ---
obs0.18566 27568 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.721 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.62 Å2
2---0.37 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.9→58.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 0 137 3063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023059
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.9734145
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5175393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.725.036137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.70815541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8561510
X-RAY DIFFRACTIONr_chiral_restr0.1250.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212302
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 95 -
Rwork0.227 1983 -
obs--98.76 %

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