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- PDB-5ixg: Crystal Structure of Burkholderia cenocepacia BcnB -

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Basic information

Entry
Database: PDB / ID: 5ixg
TitleCrystal Structure of Burkholderia cenocepacia BcnB
ComponentsYceI
KeywordsUNKNOWN FUNCTION / beta barrel lipocalin
Function / homology
Function and homology information


Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-OTP / DI(HYDROXYETHYL)ETHER / YceI
Similarity search - Component
Biological speciesBurkholderia cenocepacia PC184 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsLoutet, S.A. / Murphy, M.E.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-49597 Canada
CitationJournal: MBio / Year: 2017
Title: Antibiotic Capture by Bacterial Lipocalins Uncovers an Extracellular Mechanism of Intrinsic Antibiotic Resistance.
Authors: El-Halfawy, O.M. / Klett, J. / Ingram, R.J. / Loutet, S.A. / Murphy, M.E. / Martin-Santamaria, S. / Valvano, M.A.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Data collection / Database references
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: YceI
C: YceI
A: YceI
D: YceI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2309
Polymers74,2324
Non-polymers2,9985
Water8,683482
1
B: YceI
A: YceI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6685
Polymers37,1162
Non-polymers1,5523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-6 kcal/mol
Surface area14380 Å2
MethodPISA
2
C: YceI
D: YceI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5624
Polymers37,1162
Non-polymers1,4462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-11 kcal/mol
Surface area14340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.160, 101.170, 63.490
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
YceI


Mass: 18557.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia PC184 (bacteria)
Gene: BCPG_01022 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A2VST2
#2: Chemical
ChemComp-OTP / (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE / OCTAPRENYL PYROPHOSPHATE


Mass: 722.911 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H68O7P2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: HEPES, PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.6→37.33 Å / Num. obs: 82019 / % possible obs: 97.3 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
1.6-1.633.10.2983495178.7
8.47-37.33.20.042170.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.94 Å37.3 Å
Translation1.94 Å37.3 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
Aimless0.1.26data scaling
PHASER2.5.5phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WUB

1wub


Resolution: 1.6→37.33 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.263 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19448 4090 5 %RANDOM
Rwork0.16017 ---
obs0.16189 77882 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.251 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å2-0 Å20.07 Å2
2--0.65 Å20 Å2
3---0.52 Å2
Refinement stepCycle: 1 / Resolution: 1.6→37.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5218 0 203 482 5903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0195623
X-RAY DIFFRACTIONr_bond_other_d0.0010.025376
X-RAY DIFFRACTIONr_angle_refined_deg2.3911.9847594
X-RAY DIFFRACTIONr_angle_other_deg0.953.00212429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4715689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.02124.254228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02715923
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1761517
X-RAY DIFFRACTIONr_chiral_restr0.1430.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216284
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021263
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_it1.861.3542735
X-RAY DIFFRACTIONr_mcbond_other1.861.3532734
X-RAY DIFFRACTIONr_mcangle_it2.8122.0253425
X-RAY DIFFRACTIONr_mcangle_other2.8122.0263426
X-RAY DIFFRACTIONr_scbond_it3.4651.9062888
X-RAY DIFFRACTIONr_scbond_other3.4651.9072889
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2272.6784164
X-RAY DIFFRACTIONr_long_range_B_refined7.04413.0346346
X-RAY DIFFRACTIONr_long_range_B_other7.03212.986319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 252 -
Rwork0.187 4728 -
obs--80.39 %
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)
10.35550.09760.01630.0361-0.03380.2235-0.05080.0214-0.0162-0.00590.0128-0.0072-0.0140.00610.0380.03940.0042-0.0030.02610.00510.040147.777927.81483.7445
20.2715-0.0343-0.12710.0274-0.06940.60510.02220.01210.0756-0.02770.02130.01020.1278-0.0412-0.04350.0418-0.005-0.00660.04170.02690.056550.327736.017332.6319
30.5982-0.0549-0.01740.12240.09010.0686-0.04350.0328-0.01450.02970.01330.03310.01450.0110.03030.03920.0009-0.00420.03530.01690.0371.982527.21024.1988
40.51350.2542-0.49250.4805-0.40720.54960.0811-0.11280.0793-0.0892-0.02240.037-0.00710.1044-0.05870.0629-0.00840.02640.05410.00820.038568.947248.619424.7134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B6 - 174
2X-RAY DIFFRACTION2C6 - 174
3X-RAY DIFFRACTION3A7 - 174
4X-RAY DIFFRACTION4D6 - 174

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