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- PDB-4ki3: 1.70 Angstrom resolution crystal structure of outer-membrane lipo... -

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Basic information

Entry
Database: PDB / ID: 4ki3
Title1.70 Angstrom resolution crystal structure of outer-membrane lipoprotein carrier protein (lolA) from Yersinia pestis CO92
ComponentsOuter-membrane lipoprotein carrier protein
KeywordsCHAPERONE / IDP02066 / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases
Function / homologyLipoprotein localisation LolA/LolB/LppX / outer membrane lipoprotein receptor (LolB), chain A / Clam / Mainly Beta / ACETATE ION / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesYersinia pestis biovar Medievalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHalavaty, A.S. / Wawrzak, Z. / Kudritska, M. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.70 Angstrom resolution crystal structure of outer-membrane lipoprotein carrier protein (lolA) from Yersinia pestis CO92
Authors: Halavaty, A.S. / Wawrzak, Z. / Kudritska, M. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer-membrane lipoprotein carrier protein
B: Outer-membrane lipoprotein carrier protein
C: Outer-membrane lipoprotein carrier protein
D: Outer-membrane lipoprotein carrier protein
E: Outer-membrane lipoprotein carrier protein
F: Outer-membrane lipoprotein carrier protein
G: Outer-membrane lipoprotein carrier protein
H: Outer-membrane lipoprotein carrier protein
I: Outer-membrane lipoprotein carrier protein
J: Outer-membrane lipoprotein carrier protein
K: Outer-membrane lipoprotein carrier protein
L: Outer-membrane lipoprotein carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,51624
Polymers244,60012
Non-polymers91612
Water26,9681497
1
A: Outer-membrane lipoprotein carrier protein
B: Outer-membrane lipoprotein carrier protein
D: Outer-membrane lipoprotein carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6329
Polymers61,1503
Non-polymers4816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Outer-membrane lipoprotein carrier protein
E: Outer-membrane lipoprotein carrier protein
F: Outer-membrane lipoprotein carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2094
Polymers61,1503
Non-polymers591
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Outer-membrane lipoprotein carrier protein
H: Outer-membrane lipoprotein carrier protein
I: Outer-membrane lipoprotein carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4197
Polymers61,1503
Non-polymers2694
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Outer-membrane lipoprotein carrier protein
K: Outer-membrane lipoprotein carrier protein
L: Outer-membrane lipoprotein carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2564
Polymers61,1503
Non-polymers1061
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.201, 67.130, 132.563
Angle α, β, γ (deg.)94.30, 94.01, 120.01
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Outer-membrane lipoprotein carrier protein


Mass: 20383.354 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis biovar Medievalis (bacteria)
Strain: Harbin 35 / Gene: lolA, YPC_2798 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: E8P443
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1497 / 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: 2.09 Å3/Da / Density % sol: 41.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350 20% w/v NH4 dihydrogen Phosphate 0.2M, protein at 34 mg/mL, cryo- 20% glycerol+paratone, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 9, 2013 / Details: Be-Lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.749
11-K, -H, -L20.251
ReflectionResolution: 1.7→30 Å / Num. all: 207123 / Num. obs: 207123 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.22
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.7 / Num. unique all: 10516 / % possible all: 95.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KSN

3ksn


Resolution: 1.7→29.09 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.607 / SU ML: 0.082 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23956 10490 5.1 %RANDOM
Rwork0.20355 ---
obs0.20539 196543 93.77 %-
all-196543 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.516 Å2
Baniso -1Baniso -2Baniso -3
1--12.08 Å2-0.36 Å20.27 Å2
2---10.36 Å2-0.37 Å2
3---22.43 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16593 0 61 1497 18151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02218241
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212084
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.93424977
X-RAY DIFFRACTIONr_angle_other_deg0.841329677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.63752337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.93125.524869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.712152988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7361563
X-RAY DIFFRACTIONr_chiral_restr0.0940.22702
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02121081
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023650
X-RAY DIFFRACTIONr_mcbond_it1.1731.511324
X-RAY DIFFRACTIONr_mcbond_other0.4051.54462
X-RAY DIFFRACTIONr_mcangle_it1.863218555
X-RAY DIFFRACTIONr_scbond_it2.99536917
X-RAY DIFFRACTIONr_scangle_it4.3354.56422
LS refinement shellResolution: 1.7→1.738 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 720 -
Rwork0.222 12651 -
obs-12651 81.95 %

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