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

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Basic information

Entry
Database: PDB / ID: 2guv
TitleConformational Transition between Four- and Five-stranded Phenylalanine Zippers Determined by a Local Packing Interaction
ComponentsMajor outer membrane lipoprotein
KeywordsUNKNOWN FUNCTION / LIPOPROTEIN / PROTEIN FOLDING / PENTAMER / 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 / MOLECULAR REPLACEMENT / Resolution: 1.4 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 / 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 1.4Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Major outer membrane lipoprotein
B: Major outer membrane lipoprotein
C: Major outer membrane lipoprotein
D: Major outer membrane lipoprotein
E: Major outer membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)33,9215
Polymers33,9215
Non-polymers00
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13720 Å2
ΔGint-100 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.890, 48.847, 68.331
Angle α, β, γ (deg.)90.00, 100.53, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a pentamer.

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Components

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


Mass: 6784.220 Da / Num. of mol.: 5
Mutation: I6F, L9F, V13F, L16F, V20F, L23F, V27F, 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.: 246 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 15% isopropanol, 1,4-butanediol, 23% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 23, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→67.1 Å / Num. all: 40518 / Num. obs: 40518 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 13.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2034 / Rsym value: 0.323 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GUS

2gus


Resolution: 1.4→67.1 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.241 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.091 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 4071 10 %RANDOM
Rwork0.19296 ---
all0.1986 36447 --
obs0.19868 36447 96.3 %-
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: 22.626 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20.26 Å2
2---0.08 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.4→67.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 0 246 2666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222490
X-RAY DIFFRACTIONr_angle_refined_deg1.251.8583325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0945275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.88623.947190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96615375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7471520
X-RAY DIFFRACTIONr_chiral_restr0.0920.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022130
X-RAY DIFFRACTIONr_nbd_refined0.2140.21232
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21817
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2198
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.271
X-RAY DIFFRACTIONr_mcbond_it0.9891.51422
X-RAY DIFFRACTIONr_mcangle_it1.66422215
X-RAY DIFFRACTIONr_scbond_it2.82231178
X-RAY DIFFRACTIONr_scangle_it4.1064.51110
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 273 -
Rwork0.271 2675 -
obs-2948 95.1 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6165-0.0224-2.77450.19960.06146.73360.11260.04060.05120.0162-0.039-0.0011-0.4171-0.1508-0.0736-0.10750.01140.0117-0.0975-0.0134-0.14755.36115.40424.381
22.4131-0.4522-2.95680.31290.60024.3270.04060.1144-0.028-0.0377-0.03490.0142-0.1475-0.1652-0.0058-0.13570.00230.0134-0.1099-0.0074-0.14351.3628.82521.944
34.7682-0.5074-5.11080.21450.6226.2893-0.15630.1535-0.19790.0027-0.06040.03280.1318-0.14440.2167-0.13550.00290.0209-0.12-0.0032-0.12625.192.46124.454
46.27470.9017-6.42220.2409-0.94897.3303-0.1952-0.2154-0.2804-0.0195-0.0632-0.02350.15270.27770.2585-0.13320.00360.0191-0.10280.0134-0.121411.4734.64428.522
52.79410.5787-4.37640.2405-1.24278.90650.0634-0.1906-0.01860.0167-0.0754-0.0007-0.12710.24120.012-0.1007-0.01930.0094-0.1071-0.0066-0.141111.30312.93828.601
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 561 - 56
2X-RAY DIFFRACTION2BB1 - 561 - 56
3X-RAY DIFFRACTION3CC1 - 561 - 56
4X-RAY DIFFRACTION4DD1 - 561 - 56
5X-RAY DIFFRACTION5EE1 - 561 - 56

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