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- PDB-2hdi: Crystal structure of the Colicin I receptor Cir from E.coli in co... -

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Basic information

Entry
Database: PDB / ID: 2hdi
TitleCrystal structure of the Colicin I receptor Cir from E.coli in complex with receptor binding domain of Colicin Ia.
Components
  • Colicin I receptor
  • Colicin-Ia
KeywordsProtein Transport / Antimicrobial Protein / Outer membrane / Iron transport / TonB box / Signal transduction / Colicin I Receptor / Receptor Ligand / Membrane Protein
Function / homology
Function and homology information


siderophore-iron transmembrane transporter activity / pore-forming activity / colicin transmembrane transporter activity / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / transmembrane transporter complex / cell outer membrane / defense response to Gram-negative bacterium / killing of cells of another organism / intracellular iron ion homeostasis ...siderophore-iron transmembrane transporter activity / pore-forming activity / colicin transmembrane transporter activity / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / transmembrane transporter complex / cell outer membrane / defense response to Gram-negative bacterium / killing of cells of another organism / intracellular iron ion homeostasis / membrane / plasma membrane
Similarity search - Function
Colicin Ia; domain 2 / Colicin Ia; domain 2 / Channel forming colicin, N-terminal domain superfamily / Channel forming colicin, central receptor recognition / Colicin Ia / Channel forming colicin, C-terminal cytotoxic / Channel forming colicin, C-terminal domain superfamily / Colicin pore forming domain / Channel forming colicins signature. / TonB-dependent receptor (TBDR) proteins signature 1. ...Colicin Ia; domain 2 / Colicin Ia; domain 2 / Channel forming colicin, N-terminal domain superfamily / Channel forming colicin, central receptor recognition / Colicin Ia / Channel forming colicin, C-terminal cytotoxic / Channel forming colicin, C-terminal domain superfamily / Colicin pore forming domain / Channel forming colicins signature. / TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, plug domain / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Maltoporin; Chain A / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Beta Complex / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Colicin-Ia / Colicin I receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBuchanan, S.K. / Esser, L. / Lukacik, P.
CitationJournal: Embo J. / Year: 2007
Title: Structure of colicin I receptor bound to the R-domain of colicin Ia: implications for protein import.
Authors: Buchanan, S.K. / Lukacik, P. / Grizot, S. / Ghirlando, R. / Ali, M.M. / Barnard, T.J. / Jakes, K.S. / Kienker, P.K. / Esser, L.
History
DepositionJun 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: 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 / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Colicin I receptor
B: Colicin-Ia
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6444
Polymers84,1862
Non-polymers4592
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.633, 130.494, 56.261
Angle α, β, γ (deg.)90.00, 101.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Colicin I receptor


Mass: 71294.242 Da / Num. of mol.: 1 / Fragment: Colicin I receptor / Mutation: W338M, L343M, F589M, V591M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cirA / Plasmid: pET20b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17315
#2: Protein Colicin-Ia


Mass: 12891.374 Da / Num. of mol.: 1 / Fragment: R domain of Colicin Ia
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cia / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06716
#3: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 9 G/L PROTEIN IN 0.02M TRIS PH7.5, 0.2M NACL, 0.05% LDAO, 0.45% C8E4, 3% HEPTANETRIOL MIXED AT 1:1 RATIO WITH 0.1M MES PH6.2, 10% GLYCEROL, 22% PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 24, 2004
RadiationMonochromator: Si 220 (Rosenbaum-Rock double-crystal monochromator)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 32311 / Num. obs: 32311 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 15.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.73 / Num. unique all: 3632 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HDF

2hdf


Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.897 / SU B: 9.389 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.48 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24929 1550 5 %RANDOM
Rwork0.18781 ---
all0.19097 29295 --
obs0.19097 29295 95.42 %-
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: 44.618 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-0.61 Å2
2---0.93 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5510 0 19 255 5784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225705
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.9417739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3095709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31724.326282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0115938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8831540
X-RAY DIFFRACTIONr_chiral_restr0.0930.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024417
X-RAY DIFFRACTIONr_nbd_refined0.2050.22237
X-RAY DIFFRACTIONr_nbtor_refined0.30.23782
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2348
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.213
X-RAY DIFFRACTIONr_mcbond_it2.46943582
X-RAY DIFFRACTIONr_mcangle_it3.61355648
X-RAY DIFFRACTIONr_scbond_it6.22792435
X-RAY DIFFRACTIONr_scangle_it8.066112089
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 91 -
Rwork0.217 1638 -
obs--73.83 %
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)
10.3880.55530.20132.377-0.23551.8621-0.03550.0456-0.20210.0241-0.0181-0.3288-0.02570.32740.0536-0.0013-0.0055-0.01270.0198-0.02930.034832.3945-20.263813.96
20.73970.29830.11590.848-0.13320.3266-0.00070.0821-0.1392-0.05790.0121-0.10530.00190.0538-0.0114-0.07570.00430.0155-0.0472-0.0326-0.084833.0705-16.971715.2132
35.4744-0.09150.38070.65610.07721.17150.01110.51520.3994-0.0236-0.0993-0.11990.02180.13930.0883-0.02350.0484-0.0035-0.06370.0555-0.11465.00511.161913.6688
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA31 - 1607 - 136
2X-RAY DIFFRACTION2AA161 - 663137 - 639
3X-RAY DIFFRACTION3BB282 - 38410 - 112

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