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- PDB-2y1b: Crystal structure of the E. coli outer membrane lipoprotein RcsF -

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Basic information

Entry
Database: PDB / ID: 2y1b
TitleCrystal structure of the E. coli outer membrane lipoprotein RcsF
ComponentsPUTATIVE OUTER MEMBRANE PROTEIN, SIGNAL
KeywordsMEMBRANE PROTEIN / RCS / PHOSPHORELAY / MUCOIDITY / COLANIC ACID / CAPSULE
Function / homology
Function and homology information


: / positive regulation of phosphorelay signal transduction system / periplasmic side of cell outer membrane / outer membrane protein complex / cellular response to cell envelope stress / cell outer membrane / outer membrane-bounded periplasmic space / intracellular signal transduction / signal transduction
Similarity search - Function
Outer membrane lipoprotein RcsF / RcsF lipoprotein / Hypothetical protein apc22750. Chain B / Translation Initiation Factor IF3 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-I3C / Outer membrane lipoprotein RcsF / Outer membrane lipoprotein RcsF
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsDeclercq, J.P. / Leverrier, P. / Boujtat, A. / Collet, J.F.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of the Outer Membrane Protein Rcsf, a New Substrate for the Periplasmic Protein- Disulfide Isomerase Dsbc.
Authors: Leverrier, P. / Declercq, J.P. / Denoncin, K. / Vertommen, D. / Hiniker, A. / Cho, S.H. / Collet, J.F.
History
DepositionDec 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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: PUTATIVE OUTER MEMBRANE PROTEIN, SIGNAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4213
Polymers13,7661
Non-polymers6552
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.714, 55.714, 61.679
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2015-

HOH

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Components

#1: Protein PUTATIVE OUTER MEMBRANE PROTEIN, SIGNAL / RCSF PROTEIN


Mass: 13765.681 Da / Num. of mol.: 1 / Fragment: PERIPLASMIC DOMAIN, RESIDUES 17-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Variant: MC1000 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA GAMI / References: UniProt: A1A7P0, UniProt: P69411*PLUS
#2: Chemical ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H4I3NO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details5-AMINO-2,4,6-TRIIODOISOPHTHALIC ACID (I3C): THIS MOLECULE IS THE MAGIC TRIANGLE DESCRIBED BY ...5-AMINO-2,4,6-TRIIODOISOPHTHALIC ACID (I3C): THIS MOLECULE IS THE MAGIC TRIANGLE DESCRIBED BY TOBIAS BECK ET AL. ACTA CRYST. 2008, D64, 1179-1182
Sequence detailsRCSF WAS CLONED WITHOUT THE SEQUENCE CORRESPONDING TO THE PUTATIVE LIPOBOX.

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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: 1.92 Å3/Da / Density % sol: 36 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5
Details: HANGING DROP: PROTEIN 11MG/ML MIXED WITH I3C 20 MM RESERVOIR: 1.8M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.5, DROP: 1 MICROL AND 1 MICROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97791, 1.5
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 7, 2010 / Details: MIRROR 2 VERTICALLY FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL SI(111), HORIZONTALLY FOCUSSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.977911
21.51
ReflectionResolution: 2→19 Å / Num. obs: 7786 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→48.25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.568 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25752 358 4.6 %RANDOM
Rwork0.19644 ---
obs0.19913 7428 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.541 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20.77 Å20 Å2
2--1.54 Å20 Å2
3----2.31 Å2
Refinement stepCycle: LAST / Resolution: 2→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms636 0 21 46 703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022667
X-RAY DIFFRACTIONr_bond_other_d0.0010.02441
X-RAY DIFFRACTIONr_angle_refined_deg2.1572.007908
X-RAY DIFFRACTIONr_angle_other_deg1.04831084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.614585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94724.425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59815110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.583155
X-RAY DIFFRACTIONr_chiral_restr0.1190.2102
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021739
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02114
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2481.5429
X-RAY DIFFRACTIONr_mcbond_other0.2771.5171
X-RAY DIFFRACTIONr_mcangle_it2.372694
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6033238
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.0134.5214
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 22 -
Rwork0.254 552 -
obs--99.14 %

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