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- PDB-5fly: The FhuD protein from S.pseudintermedius -

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Basic information

Entry
Database: PDB / ID: 5fly
TitleThe FhuD protein from S.pseudintermedius
ComponentsFerrichrome ABC transporter substrate-binding protein
KeywordsMETAL TRANSPORT / STAPHYLOCOCCAL DISEASE / SIDEROPHORE / TRANSPORT / IRON / CLASS III SOLUTE BINDING PROTEIN
Function / homology
Function and homology information


ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL / : / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesStaphylococcus pseudintermedius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.598 Å
AuthorsMalito, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal Structure of Fhud at 1.6 Angstrom Resolution: A Ferrichrome-Binding Protein from the Animal and Human Pathogen Staphylococcus Pseudintermedius
Authors: Abate, F. / Cozzi, R. / Maritan, M. / Lo Surdo, P. / Maione, D. / Malito, E. / Bottomley, M.J.
History
DepositionOct 29, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 2.0Sep 25, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_src_gen / pdbx_database_status / struct_ref / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _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

Downloads & links

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Assembly

Deposited unit
A: Ferrichrome ABC transporter substrate-binding protein
B: Ferrichrome ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,00429
Polymers63,6562
Non-polymers2,34827
Water13,601755
1
A: Ferrichrome ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,05815
Polymers31,8281
Non-polymers1,23014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferrichrome ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,94614
Polymers31,8281
Non-polymers1,11813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.582, 53.822, 120.248
Angle α, β, γ (deg.)90.00, 99.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ferrichrome ABC transporter substrate-binding protein


Mass: 31827.955 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus pseudintermedius (bacteria)
Gene: DD902_02645 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A2P5JFB2
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-7PG / 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL


Mass: 384.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H36O9
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 755 / 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: 2.19 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 4.6
Details: 0.1 M CDCL2 30 % V/V PEG 400 0.1 M NA ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 13, 2012 / Details: MIRRORS TOROIDAL FOCUSING
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→49.02 Å / Num. obs: 241352 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 12.28 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.66
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.86 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B8Y

4b8y


Resolution: 1.598→49.019 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 3650 5 %
Rwork0.184 --
obs0.1857 72391 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.9 Å2
Refinement stepCycle: LAST / Resolution: 1.598→49.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4422 0 70 755 5247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084587
X-RAY DIFFRACTIONf_angle_d1.0856140
X-RAY DIFFRACTIONf_dihedral_angle_d12.8511736
X-RAY DIFFRACTIONf_chiral_restr0.04666
X-RAY DIFFRACTIONf_plane_restr0.005779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5982-1.61930.31241220.28092337X-RAY DIFFRACTION88
1.6193-1.64150.27551410.26252615X-RAY DIFFRACTION99
1.6415-1.66490.2951400.25752641X-RAY DIFFRACTION99
1.6649-1.68980.26831510.23662656X-RAY DIFFRACTION99
1.6898-1.71620.26981490.24722548X-RAY DIFFRACTION99
1.7162-1.74430.28731240.24052726X-RAY DIFFRACTION99
1.7443-1.77440.22751310.22762621X-RAY DIFFRACTION100
1.7744-1.80670.25141480.21242630X-RAY DIFFRACTION100
1.8067-1.84140.22141430.20932631X-RAY DIFFRACTION100
1.8414-1.8790.25681430.19312652X-RAY DIFFRACTION100
1.879-1.91990.21151400.18742661X-RAY DIFFRACTION100
1.9199-1.96450.20391270.18792650X-RAY DIFFRACTION100
1.9645-2.01360.21081220.18372677X-RAY DIFFRACTION100
2.0136-2.06810.22691470.17972671X-RAY DIFFRACTION100
2.0681-2.12890.21541320.18082620X-RAY DIFFRACTION100
2.1289-2.19770.22351370.17262669X-RAY DIFFRACTION100
2.1977-2.27620.20441460.16462659X-RAY DIFFRACTION100
2.2762-2.36730.20421570.16762632X-RAY DIFFRACTION100
2.3673-2.47510.21851430.17192669X-RAY DIFFRACTION100
2.4751-2.60560.23271400.1712653X-RAY DIFFRACTION100
2.6056-2.76880.23331490.17472676X-RAY DIFFRACTION100
2.7688-2.98250.23731460.18432638X-RAY DIFFRACTION100
2.9825-3.28260.21931410.17882683X-RAY DIFFRACTION99
3.2826-3.75750.1821360.15152689X-RAY DIFFRACTION100
3.7575-4.73340.15941490.14762673X-RAY DIFFRACTION99
4.7334-49.04230.1971460.19192764X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 16.8987 Å / Origin y: -12.1227 Å / Origin z: 29.4013 Å
111213212223313233
T0.0751 Å2-0.0019 Å20.0294 Å2-0.0746 Å2-0.0046 Å2--0.0852 Å2
L0.2421 °2-0.161 °20.2306 °2-0.2618 °2-0.219 °2--0.3712 °2
S0.0063 Å °0.0023 Å °0.0042 Å °0.0011 Å °-0.0073 Å °-0.0002 Å °0.0101 Å °0.0121 Å °-0.0009 Å °
Refinement TLS groupSelection details: ALL

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