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- PDB-5amu: IglE I39A,Y40A,V44A -

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Basic information

Entry
Database: PDB / ID: 5amu
TitleIglE I39A,Y40A,V44A
ComponentsIGLE
KeywordsUNKNOWN FUNCTION / TYPE SIX SECRETION SYSTEM / LIPOPROTEIN
Function / homology: / IglE, N-terminal domain / symbiont cell surface / Prokaryotic membrane lipoprotein lipid attachment site profile. / host cell cytoplasm / Type VI lipoprotein IgE-like C-terminal domain-containing protein
Function and homology information
Biological speciesFRANCISELLA NOVICIDA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRobb, C.S. / Nano, F.E. / Boraston, A.B.
CitationJournal: To be Published
Title: The Structure, Dimerisation and Impact on Intramacrophage Replication of Igle in Francisella Novicida
Authors: Robb, C.S. / Nano, F.E. / Boraston, A.B.
History
DepositionSep 1, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: IGLE
B: IGLE


Theoretical massNumber of molelcules
Total (without water)28,6622
Polymers28,6622
Non-polymers00
Water1,65792
1
A: IGLE


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: IGLE


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.560, 53.780, 51.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein IGLE


Mass: 14331.027 Da / Num. of mol.: 2 / Fragment: UNIPROT RESIDUES 25-125 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FRANCISELLA NOVICIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: A0Q7H2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.79 Å3/Da / Description: NONE

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→22.07 Å / Num. obs: 10932 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AMT

5amt


Resolution: 2.2→21.82 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.659 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26499 524 4.8 %RANDOM
Rwork0.19831 ---
obs0.2017 10372 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.21 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å20 Å20 Å2
2---0.17 Å20 Å2
3----1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.2→21.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 0 92 1629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021565
X-RAY DIFFRACTIONr_bond_other_d0.0010.021412
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9612129
X-RAY DIFFRACTIONr_angle_other_deg0.83633244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0635195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6626.43873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66615249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.204152
X-RAY DIFFRACTIONr_chiral_restr0.0920.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211795
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02339
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 36 -
Rwork0.203 763 -
obs--99.88 %

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