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- PDB-2gus: Conformational Transition between Four- and Five-stranded Phenyla... -

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Basic information

Entry
Database: PDB / ID: 2gus
TitleConformational Transition between Four- and Five-stranded Phenylalanine Zippers Determined by a Local Packing Interaction
ComponentsMajor outer membrane lipoprotein
KeywordsUNKNOWN FUNCTION / Lipoprotein / protein folding / tetramer / phenylalanine-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 / MAD / Resolution: 1.75 Å
AuthorsLiu, J. / Zheng, Q. / Deng, Y. / Kallenbach, N.R. / Lu, M.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Conformational Transition between Four and Five-stranded Phenylalanine Zippers Determined by a Local Packing Interaction.
Authors: Liu, J. / Zheng, Q. / Deng, Y. / Kallenbach, N.R. / Lu, M.
History
DepositionMay 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 20, 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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major outer membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)6,7681
Polymers6,7681
Non-polymers00
Water45025
1
A: Major outer membrane lipoprotein

A: Major outer membrane lipoprotein

A: Major outer membrane lipoprotein

A: Major outer membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)27,0734
Polymers27,0734
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area7490 Å2
ΔGint-58 kcal/mol
Surface area9170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)37.002, 37.002, 80.949
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-57-

HOH

DetailsThe biological assembly is a tetramer.

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Components

#1: Protein Major outer membrane lipoprotein / Murein-lipoprotein


Mass: 6768.242 Da / Num. of mol.: 1
Mutation: I6F, L9F, V13F, L16F, V20F, L23F, V27M, M30F, V34F, A37F, A41F, A44F, L48F, M51F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lpp, mlpA, mulI / Plasmid: pF14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/pLyss / References: UniProt: P69776
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, 10mM nickel chloride, 14% PEG MME2000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793, 0.9796, 0.9681
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 2005
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97961
30.96811
ReflectionResolution: 1.75→80.85 Å / Num. all: 6157 / Num. obs: 6157 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 17
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 4.4 / Num. unique all: 578 / Rsym value: 0.404 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→80.85 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.894 / SU B: 4.129 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28702 600 9.7 %RANDOM
Rwork0.23795 ---
all0.243 6157 --
obs0.24303 5557 99.08 %-
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: 38.101 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--0.61 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.75→80.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms364 0 0 25 389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022374
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.849498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.434541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60724.13829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.791558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.993153
X-RAY DIFFRACTIONr_chiral_restr0.1040.244
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02316
X-RAY DIFFRACTIONr_nbd_refined0.2050.2152
X-RAY DIFFRACTIONr_nbtor_refined0.3190.2274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.218
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.330.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2980.28
X-RAY DIFFRACTIONr_mcbond_it1.1051.5214
X-RAY DIFFRACTIONr_mcangle_it1.7012330
X-RAY DIFFRACTIONr_scbond_it2.9743176
X-RAY DIFFRACTIONr_scangle_it4.1814.5168
LS refinement shellResolution: 1.745→1.791 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 35 -
Rwork0.187 376 -
obs-411 97.2 %
Refinement TLS params.Method: refined / Origin x: 4.369 Å / Origin y: 23.026 Å / Origin z: 7.512 Å
111213212223313233
T-0.2077 Å2-0.0213 Å2-0.0119 Å2--0.199 Å2-0.0012 Å2---0.1591 Å2
L2.5073 °2-0.0795 °20.981 °2-3.3164 °2-1.8613 °2--11.8661 °2
S-0.0404 Å °-0.2906 Å °0.0644 Å °0.3666 Å °0.0239 Å °-0.0617 Å °-0.3517 Å °-0.002 Å °0.0165 Å °

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