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- PDB-2r1a: Crystal structure of the periplasmic lipopolysaccharide transport... -

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Basic information

Entry
Database: PDB / ID: 2r1a
TitleCrystal structure of the periplasmic lipopolysaccharide transport protein LptA (YhbN), trigonal form
ComponentsProtein yhbN
KeywordsTRANSPORT PROTEIN / mainly beta / beta-jellyroll / beta-taco / Structural Genomics / Bacterial Structural Genomics Initiative / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


transporter complex / glycolipid transfer activity / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / lipopolysaccharide binding / cell outer membrane / outer membrane-bounded periplasmic space / periplasmic space / identical protein binding
Similarity search - Function
Lipopolysaccharide (LPS) transport protein A like domain / Lipopolysaccharide export system protein LptA / lipopolysaccharide transport protein A fold / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Sandwich / Mainly Beta
Similarity search - Domain/homology
Lipopolysaccharide export system protein LptA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.26 Å
AuthorsSuits, M.D.L. / Polissi, A. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Novel structure of the conserved gram-negative lipopolysaccharide transport protein A and mutagenesis analysis.
Authors: Suits, M.D. / Sperandeo, P. / Deho, G. / Polissi, A. / Jia, Z.
History
DepositionAug 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Protein yhbN
B: Protein yhbN
C: Protein yhbN
D: Protein yhbN
E: Protein yhbN
F: Protein yhbN
G: Protein yhbN
H: Protein yhbN


Theoretical massNumber of molelcules
Total (without water)139,1008
Polymers139,1008
Non-polymers00
Water1,22568
1
A: Protein yhbN
B: Protein yhbN
C: Protein yhbN
D: Protein yhbN


Theoretical massNumber of molelcules
Total (without water)69,5504
Polymers69,5504
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
MethodPISA
2
E: Protein yhbN
F: Protein yhbN
G: Protein yhbN
H: Protein yhbN


Theoretical massNumber of molelcules
Total (without water)69,5504
Polymers69,5504
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.210, 146.210, 186.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Protein yhbN


Mass: 17387.471 Da / Num. of mol.: 8 / Fragment: Periplasmic processed form: Residues 27-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yhbN, b3200, JW3167 / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ADV1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 4.14 Å3/Da / Density % sol: 70.32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, Glycerol, LPS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977173 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 4, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977173 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. all: 35797 / Num. obs: 30606 / % possible obs: 97.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.9 % / Rmerge(I) obs: 0.127 / Rsym value: 0.077 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.25-3.376.70.614181.8
3.37-3.56.70.353194.8
3.5-3.667.60.313199.6
3.66-3.858.70.3441100
3.85-4.099.30.3341100
4.09-4.419.60.1781100
4.41-4.859.90.08197.6
4.85-5.5610.20.1031100
5.56-710.20.0961100
7-509.50.05198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0065refinement
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2R19

2r19


Resolution: 3.26→29.98 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.777 / SU B: 27.964 / SU ML: 0.477 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.65 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.36086 1518 5 %RANDOM
Rwork0.29801 ---
obs0.3011 30606 83.64 %-
all-30606 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.266 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.32 Å20 Å2
2--0.65 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 3.26→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7552 0 0 68 7620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0217665
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0351.9310487
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76451049
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.38226.637333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.3715993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.805158
X-RAY DIFFRACTIONr_chiral_restr0.0660.21256
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215968
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_it0.2571.55248
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.47528309
X-RAY DIFFRACTIONr_scbond_it0.43332417
X-RAY DIFFRACTIONr_scangle_it0.7934.52178
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.26→3.345 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.541 27 -
Rwork0.397 638 -
obs--24.79 %
Refinement TLS params.Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å
111213212223313233
T0 Å20 Å20 Å2-0 Å20 Å2--0 Å2
L0 °20 °20 °2-0 °20 °2--0 °2
S0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °

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