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

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Basic information

Entry
Database: PDB / ID: 2hdf
TitleCrystal structure of the Colicin I receptor Cir from E.coli
ComponentsColicin I receptor
KeywordsPROTEIN TRANSPORT / Outer membrane / Iron transport / TonB box / Signal transduction / Colicin I Receptor / Membrane Protein
Function / homology
Function and homology information


siderophore-iron transmembrane transporter activity / colicin transmembrane transporter activity / siderophore transmembrane transport / siderophore uptake transmembrane transporter activity / transmembrane transporter complex / cell outer membrane / intracellular iron ion homeostasis / membrane
Similarity search - Function
TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / TonB-dependent receptor (TBDR) proteins profile. / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Vitamin B12 transporter BtuB-like ...TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / TonB-dependent receptor (TBDR) proteins profile. / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / Beta Complex / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-OCTYL-2-HYDROXYETHYL SULFOXIDE / STRONTIUM ION / Colicin I receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _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: Colicin I receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2644
Polymers71,7631
Non-polymers5003
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.593, 84.336, 99.458
Angle α, β, γ (deg.)90.00, 109.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Colicin I receptor


Mass: 71763.203 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: Chemical ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-OES / N-OCTYL-2-HYDROXYETHYL SULFOXIDE


Mass: 206.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 7-8 G/L PROTEIN IN 0.02M TRIS PH7.5, 0.001M EDTA, 0.3M NACL, 1% N-OCTYL-2-HYDROXYETHYL SULFOXIDE MIXED AT 1:1 RATIO WITH 0.1M TRIS PH7.5, 0.02-0.05M SRCL2, 5% ISOPROPANOL, 32-40 % PEG 2000 ...Details: 7-8 G/L PROTEIN IN 0.02M TRIS PH7.5, 0.001M EDTA, 0.3M NACL, 1% N-OCTYL-2-HYDROXYETHYL SULFOXIDE MIXED AT 1:1 RATIO WITH 0.1M TRIS PH7.5, 0.02-0.05M SRCL2, 5% ISOPROPANOL, 32-40 % 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: 0.97940, 0.97924, 0.97240
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2003
RadiationMonochromator: Si 220 (Rosenbaum-Rock double-crystal monochromator)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.979241
30.97241
ReflectionResolution: 2.65→30 Å / Num. all: 40440 / Num. obs: 40440 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 16.4
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 2 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 1.85 / Num. unique all: 3745 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.65→15 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.872 / SU B: 27.09 / SU ML: 0.271 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.217 / ESU R Free: 0.38
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2911 1056 5.1 %RANDOM
Rwork0.23867 ---
all0.24137 19508 --
obs0.24137 19508 99.99 %-
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: 57.581 Å2
Baniso -1Baniso -2Baniso -3
1-2.67 Å20 Å21.2 Å2
2--0.36 Å20 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 2.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4493 0 27 18 4538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224636
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.9396288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5055580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.54424.48221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.50215716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5231527
X-RAY DIFFRACTIONr_chiral_restr0.0910.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023585
X-RAY DIFFRACTIONr_nbd_refined0.2190.21725
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23026
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2200
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.23
X-RAY DIFFRACTIONr_mcbond_it1.93652888
X-RAY DIFFRACTIONr_mcangle_it3.31164629
X-RAY DIFFRACTIONr_scbond_it4.05671846
X-RAY DIFFRACTIONr_scangle_it6.136121659
LS refinement shellResolution: 2.65→2.717 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 72 -
Rwork0.269 1407 -
obs--99.93 %
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)
14.0342-0.5638-1.33592.3894-0.45983.44170.10030.14420.2751-0.2250.11480.0641-0.1191-0.3664-0.21510.01860.0171-0.02180.0205-0.0220.038421.14710.148222.4539
20.9137-0.3963-0.10671.0035-0.17291.6406-0.01180.04040.1062-0.10390.0479-0.00680.05-0.2183-0.036-0.1651-0.0017-0.0493-0.12050.0117-0.155120.241810.132918.78
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

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