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- PDB-5ffp: Crystal structure of CdiI from Burkholderia dolosa AUO158 -

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Basic information

Entry
Database: PDB / ID: 5ffp
TitleCrystal structure of CdiI from Burkholderia dolosa AUO158
ComponentsImmunity 23 family protein
KeywordsANTITOXIN / immunity protein / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes / UC4CDI
Biological speciesBurkholderia dolosa AU0158 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsMichalska, K. / Stols, L. / Eschenfeldt, W. / Goulding, C.W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102318 United States
CitationJournal: To Be Published
Title: Crystal structure of CdiI from Burkholderia dolosa AUO158
Authors: Michalska, K. / Stols, L. / Eschenfeldt, W. / Goulding, C.W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionDec 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunity 23 family protein
B: Immunity 23 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9983
Polymers38,7592
Non-polymers2381
Water905
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-7 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.298, 116.298, 70.065
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1 - 155 / Label seq-ID: 1 - 155

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsAUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN AT THIS STAGE

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Components

#1: Protein Immunity 23 family protein


Mass: 19379.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia dolosa AU0158 (bacteria) / Gene: AK34_4389 / Plasmid: pMCSG58 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.57 Å3/Da / Density % sol: 65.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M (NH4)2SO4, 0.1 sodium acetate pH 5.6, 30% PEG 4000, cryo saturated sucrose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2014 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.572
11K, H, -L20.428
ReflectionResolution: 2.5→30.01 Å / Num. obs: 18768 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 1.83 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→30.01 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.105 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Refinement performed against intensities.
RfactorNum. reflection% reflectionSelection details
Rfree0.20492 1861 9.9 %thin resolution shells
Rwork0.19044 ---
obs0.19191 16893 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.16 Å2
Baniso -1Baniso -2Baniso -3
1-14.4 Å20 Å20 Å2
2--14.4 Å20 Å2
3----28.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 15 5 2440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192491
X-RAY DIFFRACTIONr_bond_other_d0.0040.022238
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9563372
X-RAY DIFFRACTIONr_angle_other_deg0.98735160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9475308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2724120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08215366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0621514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022844
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02594
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_it0.6831.2831238
X-RAY DIFFRACTIONr_mcbond_other0.6821.2821237
X-RAY DIFFRACTIONr_mcangle_it1.181.9191544
X-RAY DIFFRACTIONr_mcangle_other1.1791.9191545
X-RAY DIFFRACTIONr_scbond_it1.5791.4371253
X-RAY DIFFRACTIONr_scbond_other1.5451.4381253
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0482.0941829
X-RAY DIFFRACTIONr_long_range_B_refined3.22610.272707
X-RAY DIFFRACTIONr_long_range_B_other3.22610.2962708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8312 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.501→2.636 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.441 283 -
Rwork0.435 2392 -
obs--98.78 %
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)
10.39270.3806-1.56032.0280.27559.28850.0646-0.08060.0710.09410.03-0.1583-0.45330.3203-0.09460.22070.0646-0.03830.0631-0.05350.216955.16213.146328.2626
214.417-8.4488-7.56416.50253.96775.17170.0090.21630.2545-0.0950.0296-0.0975-0.0172-0.3878-0.03860.4610.018-0.01890.20040.03030.274352.170422.780929.2818
32.1286-1.1854-0.39316.028-5.2785.80040.06770.06340.374-0.01690.64390.5726-0.2479-0.803-0.71160.85960.2877-0.09960.2902-0.05460.530940.875520.502324.2668
44.95720.7942-0.57458.29381.95358.28290.0411-0.03860.05490.4882-0.10950.4222-0.1455-0.71180.06840.41220.21240.06090.19640.02560.216542.12815.483331.3924
513.0303-1.2627-1.42813.7150.8113.41030.0781-0.52090.2005-0.0942-0.0261-0.2082-0.56960.2202-0.05210.45740.0294-0.01360.1078-0.00810.180656.464914.97235.885
614.093-1.5978-4.21087.9914-5.02995.14170.01490.15980.29920.2123-0.077-0.2393-0.15420.0010.06210.04590.0295-0.02950.13270.06560.094436.134842.7405-7.6683
73.8424-0.00870.21511.2860.70527.47-0.0923-0.2129-0.1159-0.02880.01710.09270.041-0.15670.07530.00630.02060.01120.12540.05690.063130.428544.66194.0303
84.8442-3.3243-1.07814.67050.27920.4659-0.2399-0.4139-0.02840.4710.2418-0.5120.25240.1752-0.00190.56860.1751-0.2220.3388-0.00590.290244.011331.34690.7967
91.8072-0.53041.77372.1521-2.93967.74230.2601-0.3936-0.7920.1896-0.0150.12151.01180.2017-0.24510.47410.1412-0.03050.34150.11420.482840.430425.50195.3775
106.06840.0751-1.49265.88362.0786.87180.02060.169-0.4501-0.36290.0604-0.34130.4980.2536-0.0810.16220.1092-0.03830.196-0.01610.133939.925233.2977-4.5317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 50
2X-RAY DIFFRACTION2A51 - 68
3X-RAY DIFFRACTION3A69 - 107
4X-RAY DIFFRACTION4A108 - 135
5X-RAY DIFFRACTION5A136 - 155
6X-RAY DIFFRACTION6B1 - 11
7X-RAY DIFFRACTION7B12 - 43
8X-RAY DIFFRACTION8B44 - 76
9X-RAY DIFFRACTION9B77 - 117
10X-RAY DIFFRACTION10B118 - 155

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