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- PDB-5tse: 2.35 Angstrom Crystal Structure Minor Lipoprotein from Acinetobac... -

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Basic information

Entry
Database: PDB / ID: 5tse
Title2.35 Angstrom Crystal Structure Minor Lipoprotein from Acinetobacter baumannii.
ComponentsLPS-assembly lipoprotein LptE
KeywordsLIPID BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane / lipopolysaccharide binding
Similarity search - Function
Lipoprotein like domain / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Double Stranded RNA Binding Domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / LPS-assembly lipoprotein LptE
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.35 Angstrom Crystal Structure Minor Lipoprotein from Acinetobacter baumannii.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references / Structure summary
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LPS-assembly lipoprotein LptE
B: LPS-assembly lipoprotein LptE
C: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8394
Polymers48,7933
Non-polymers461
Water1,06359
1
A: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3102
Polymers16,2641
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LPS-assembly lipoprotein LptE


Theoretical massNumber of molelcules
Total (without water)16,2641
Polymers16,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LPS-assembly lipoprotein LptE


Theoretical massNumber of molelcules
Total (without water)16,2641
Polymers16,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.806, 68.806, 96.586
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein LPS-assembly lipoprotein LptE


Mass: 16264.305 Da / Num. of mol.: 3 / Fragment: UNP residues 30-169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: lptE, A7A43_01670, AB988_1847, ACX60_15420, APD31_17935, AQ480_10880, AQ482_00945, AZE33_02665, IOMTU433_3277, IX87_17195, LV38_00030, TE32_16750
Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: V5VH20
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 15.9 mg/ml, 0.01M Tris HCl (pH 8.3), Screen: JCSG+ (A8), 0.2M Ammonium formate, 20% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2016
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 18791 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 63.4 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 31.5
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.682 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BF2

3bf2


Resolution: 2.35→29.32 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 19.979 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.431 / ESU R Free: 0.27 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2628 953 5.1 %RANDOM
Rwork0.21569 ---
obs0.2182 17811 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 70.732 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20 Å2
2--1.58 Å20 Å2
3----3.15 Å2
Refinement stepCycle: 1 / Resolution: 2.35→29.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 3 59 3272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023256
X-RAY DIFFRACTIONr_bond_other_d0.0010.023249
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9924422
X-RAY DIFFRACTIONr_angle_other_deg0.84837433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.2765395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.45624.877162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.08515612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9811530
X-RAY DIFFRACTIONr_chiral_restr0.0810.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.023682
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02720
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_it2.4944.8791589
X-RAY DIFFRACTIONr_mcbond_other2.4934.8811590
X-RAY DIFFRACTIONr_mcangle_it3.9747.2981981
X-RAY DIFFRACTIONr_mcangle_other3.9737.3011982
X-RAY DIFFRACTIONr_scbond_it2.5325.2121667
X-RAY DIFFRACTIONr_scbond_other2.5315.2111666
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.117.7152442
X-RAY DIFFRACTIONr_long_range_B_refined7.17456.6083464
X-RAY DIFFRACTIONr_long_range_B_other7.16956.5743458
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 59 -
Rwork0.303 1307 -
obs--99.56 %
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)
13.5242-0.7894-0.82112.45310.22012.6083-0.3395-0.2327-0.1660.19750.36260.30010.1494-0.1673-0.02310.04490.03260.02830.0790.05870.1602-5.4506-21.0145-25.5452
26.2129-4.2449-4.53324.69622.40174.4526-0.3148-0.46910.1247-0.04150.336-0.27220.13890.1979-0.02120.12750.002-0.00260.1336-0.00440.10851.5834-21.1511-29.1601
35.8908-3.747-0.37797.48554.42413.5705-0.03540.00770.1664-0.13980.301-0.3727-0.08260.263-0.26560.06440.01370.02540.11060.04050.089-4.2063-19.1418-11.0899
44.4366-1.43570.12496.86381.91216.0004-0.01290.2283-0.09110.03760.01530.7235-0.0372-1.1159-0.00240.01290.0190.01640.2650.06020.1037-15.3891-27.00039.0054
56.55280.0808-5.52591.87230.46055.4211-0.1709-0.25950.27990.17410.2497-0.1796-0.13390.2324-0.07880.25860.1056-0.04930.08120.00640.224-0.7706-19.49756.824
62.9455-0.5527-3.20381.3990.68726.2206-0.0902-0.12670.0066-0.14260.1994-0.2877-0.1001-0.0443-0.10920.17660.02260.02020.0484-0.03060.16630.9866-27.46053.7925
73.8302-1.18031.40355.4528-1.79825.3438-0.1756-0.0098-0.21310.97380.18740.0525-0.0050.2564-0.01190.21860.04880.07860.0298-0.01350.204810.8338-44.8709-7.4345
84.4822-2.3831.45811.81310.19884.2305-0.1303-0.1897-0.4810.30010.00010.4210.429-0.67850.13020.1456-0.06260.12080.13130.02890.3928-5.1393-49.1121-11.0444
93.6755-1.61445.59042.1166-3.191610.1919-0.0568-0.0784-0.22990.0840.21230.41920.0078-0.2801-0.15550.079-0.00020.09580.02770.0240.2302-3.779-40.6032-13.7195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 98
2X-RAY DIFFRACTION2A99 - 156
3X-RAY DIFFRACTION3A157 - 169
4X-RAY DIFFRACTION4B36 - 81
5X-RAY DIFFRACTION5B82 - 119
6X-RAY DIFFRACTION6B120 - 169
7X-RAY DIFFRACTION7C37 - 81
8X-RAY DIFFRACTION8C82 - 124
9X-RAY DIFFRACTION9C125 - 167

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