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- PDB-2r19: Crystal structure of the periplasmic lipopolysaccharide transport... -

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Basic information

Entry
Database: PDB / ID: 2r19
TitleCrystal structure of the periplasmic lipopolysaccharide transport protein LptA (YhbN), orthorhombic form
ComponentsProtein yhbN
KeywordsTRANSPORT PROTEIN / beta-jellyroll / mainly beta / beta-taco / Structural Genomics / 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 / MAD / Resolution: 2.16 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: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Protein yhbN
B: Protein yhbN


Theoretical massNumber of molelcules
Total (without water)34,7752
Polymers34,7752
Non-polymers00
Water5,477304
1
A: Protein yhbN
B: Protein yhbN

A: Protein yhbN
B: Protein yhbN


Theoretical massNumber of molelcules
Total (without water)69,5504
Polymers69,5504
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+3/2,-y+1,z+1/21
Buried area5380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.910, 58.410, 149.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein yhbN


Mass: 17387.471 Da / Num. of mol.: 2 / 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.: 304 / 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: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, Glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
SYNCHROTRONNSLS X29A20.9796
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDApr 16, 2006
ADSC QUANTUM 3152CCDMar 16, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97961
ReflectionRedundancy: 13.2 % / Av σ(I) over netI: 3.1 / Number: 107551 / Rmerge(I) obs: 0.135 / Χ2: 0.64 / D res high: 3 Å / D res low: 50 Å / Num. obs: 8168 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.465099.810.0862.18412.8
5.136.4610010.1420.67813
4.485.1399.610.0690.62713.2
4.074.4810010.130.55813.7
3.784.0710010.2420.4813.8
3.563.7810010.2720.42313.9
3.383.5610010.4170.34213.6
3.233.3898.910.7750.30513.6
3.113.2399.610.29812.6
33.1198.510.29211.5
ReflectionResolution: 2.15→50 Å / Num. all: 23284 / Num. obs: 13258 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.061 / Χ2: 0.976 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.236.70.73923331.0061,2100
2.23-2.326.60.76323240.9191,2100
2.32-2.426.60.51523350.9271,2100
2.42-2.556.50.94623490.8681,2100
2.55-2.716.50.78123460.8511,2100
2.71-2.926.40.50923620.8391,2100
2.92-3.216.20.28123700.8721,2100
3.21-3.686.20.09823821.0771,299.7
3.68-4.636.10.04723971.1991,299.3
4.63-506.60.03125161.1891,297.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.16→46.03 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.615 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.376 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 691 5.2 %RANDOM
Rwork0.217 ---
all0.219 12567 --
obs0.219 12567 56.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.805 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.16→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 0 304 2350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222079
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.9352833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5665272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.81427.11397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1415319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.756152
X-RAY DIFFRACTIONr_chiral_restr0.1050.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021590
X-RAY DIFFRACTIONr_nbd_refined0.2560.2949
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.210
LS refinement shellResolution: 2.16→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 1 -
Rwork0.128 49 -
all-50 -
obs--2.97 %

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