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- PDB-5i0x: COPPER-BOUND M90I VARIANT OF UROPATHOGENIC ESCHERICHIA COLI STRAI... -

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Basic information

Entry
Database: PDB / ID: 5i0x
TitleCOPPER-BOUND M90I VARIANT OF UROPATHOGENIC ESCHERICHIA COLI STRAIN F11 FETP
ComponentsPeriplasmic protein-probably involved in high-affinity Fe2+ transportPeriplasm
KeywordsMETAL TRANSPORT / MUTANT / MIXED BETA SANDWICH / IRON TRANSPORT
Function / homology
Function and homology information


Periplasmic metal-binding protein Tp34-type / Periplasmic metal-binding protein Tp34-type / Periplasmic metal-binding protein Tp34-type superfamily / Fe2+ transport protein / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / : / Periplasmic protein-probably involved in high-affinity Fe2+ transport
Similarity search - Component
Biological speciesEscherichia coli F11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChan, A.C. / Murphy, M.E.
CitationJournal: Metallomics / Year: 2020
Title: A copper site is required for iron transport by the periplasmic proteins P19 and FetP.
Authors: Chan, A.C.K. / Lin, H. / Koch, D. / Grass, G. / Nies, D.H. / Murphy, M.E.P.
History
DepositionFeb 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic protein-probably involved in high-affinity Fe2+ transport
B: Periplasmic protein-probably involved in high-affinity Fe2+ transport
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4765
Polymers35,2862
Non-polymers1913
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-57 kcal/mol
Surface area14810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.155, 51.612, 66.136
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Periplasmic protein-probably involved in high-affinity Fe2+ transport / Periplasm


Mass: 17642.906 Da / Num. of mol.: 2 / Mutation: M90I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli F11 (bacteria) / Gene: EcF11_1994 / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0J9WZP9, UniProt: A0A1S4NYE6*PLUS
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.15M FORMATE, 16% PEG 3350

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL7-111
SYNCHROTRONSSRL BL7-121
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMay 7, 2010
ADSC QUANTUM 315r2CCDMay 7, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionResolution: 1.5→66.03 Å / Num. obs: 52557 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.362 / % possible all: 96.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NRQ

3nrq


Resolution: 1.5→66.03 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.268 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.078 / Details: HYDROGENS HAVE BEEN USED IF PRESENT
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2668 5.1 %RANDOM
Rwork0.176 ---
obs0.178 52538 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.14 Å2
2--0.55 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.5→66.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 3 346 2766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192721
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.953735
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86625.159126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67715435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.034157
X-RAY DIFFRACTIONr_chiral_restr0.0940.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212215
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 189 -
Rwork0.256 3361 -
obs--93.52 %

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