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- PDB-1jcd: Crystal Structure of a Novel Alanine-Zipper Trimer at 1.3 A Resol... -

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Basic information

Entry
Database: PDB / ID: 1jcd
TitleCrystal Structure of a Novel Alanine-Zipper Trimer at 1.3 A Resolution, I6A,L9A,V13A,L16A,V20A,L23A,V27A,M30A,V34A,L48A,M51A mutations
ComponentsMAJOR OUTER MEMBRANE LIPOPROTEIN
KeywordsMEMBRANE PROTEIN / LIPOPROTEIN / PROTEIN FOLDING / COILED COIL / HELIX CAPPING / ALANINE-ZIPPER
Function / homology
Function and homology information


periplasmic space organization / lipid modification / peptidoglycan binding / cell outer membrane / outer membrane-bounded periplasmic space / lipid binding / extracellular region / identical protein binding / membrane
Similarity search - Function
Lipoprotein leucine-zipper / Major outer membrane lipoprotein Lpp / Lipoprotein leucine-zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #190 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Major outer membrane lipoprotein Lpp
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsLiu, J. / Lu, M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: An Alanine-Zipper Structure Determined by Long Range Intermolecular Interactions
Authors: Liu, J. / Lu, M.
History
DepositionJun 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAJOR OUTER MEMBRANE LIPOPROTEIN
B: MAJOR OUTER MEMBRANE LIPOPROTEIN
C: MAJOR OUTER MEMBRANE LIPOPROTEIN


Theoretical massNumber of molelcules
Total (without water)15,5053
Polymers15,5053
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-27 kcal/mol
Surface area8520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)21.842, 26.935, 45.805
Angle α, β, γ (deg.)88.05, 84.95, 87.56
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a trimer.

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Components

#1: Protein MAJOR OUTER MEMBRANE LIPOPROTEIN / MUREIN-LIPOPROTEIN


Mass: 5168.225 Da / Num. of mol.: 3
Mutation: I6A,L9A,V13A,L16A,V20A,L23A,V27A,M30A,V34A,L48A,M51A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P69776
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 1.5 Å3/Da / Density % sol: 17.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Sodium acetate, sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11 mMoxidized glutathione1drop
21 mMglutathione1drop
350 mM1dropNaCl
40.1 MTris-HCl1droppH8.7
51 mMEDTA1drop
640 mg/mlprotein1drop
70.1 Msodium acetate1reservoirpH4.0
81.3 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: May 30, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 23835 / Num. obs: 23835 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 14.4
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 10.8 / Num. unique all: 2150 / % possible all: 83.3
Reflection
*PLUS
Num. measured all: 153880
Reflection shell
*PLUS
Lowest resolution: 1.32 Å

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Processing

Software
NameClassification
MADNESSdata collection
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
MADNESSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JCC

1jcc


Resolution: 1.3→22.87 Å / Num. parameters: 11157 / Num. restraintsaints: 13054 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2352 9 %RANDOM
Rwork0.149 ---
all-23835 --
obs-23835 93.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1238
Refinement stepCycle: LAST / Resolution: 1.3→22.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 0 186 1238
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.017
X-RAY DIFFRACTIONs_zero_chiral_vol0.054
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.055
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.054
X-RAY DIFFRACTIONs_approx_iso_adps0.07
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 50 Å / Num. reflection obs: 21483 / % reflection Rfree: 10 % / Rfactor all: 0.15 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2
X-RAY DIFFRACTIONs_plane_restr0.017
X-RAY DIFFRACTIONs_chiral_restr0.054

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