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- PDB-4yhb: Crystal structure of a siderophore utilization protein from T. fusca -

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Basic information

Entry
Database: PDB / ID: 4yhb
TitleCrystal structure of a siderophore utilization protein from T. fusca
ComponentsIron-chelator utilization protein
KeywordsOXIDOREDUCTASE / Siderophore utilization
Function / homology
Function and homology information


ferric-chelate reductase (NADPH) activity / cellular response to iron ion starvation / iron import into cell / siderophore transport / FAD binding / metal ion binding
Similarity search - Function
Siderophore-interacting protein / Siderophore-interacting protein, C-terminal domain / FAD-binding 9, siderophore-interacting / Siderophore-interacting protein / Siderophore-interacting FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain ...Siderophore-interacting protein / Siderophore-interacting protein, C-terminal domain / FAD-binding 9, siderophore-interacting / Siderophore-interacting protein / Siderophore-interacting FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Iron-chelator utilization protein / :
Similarity search - Component
Biological speciesThermobifida fusca TM51 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8892 Å
AuthorsLi, K. / Bruner, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM086570 United States
CitationJournal: Biochemistry / Year: 2015
Title: Structure and Mechanism of the Siderophore-Interacting Protein from the Fuscachelin Gene Cluster of Thermobifida fusca.
Authors: Li, K. / Chen, W.H. / Bruner, S.D.
History
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron-chelator utilization protein
B: Iron-chelator utilization protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,33710
Polymers61,1632
Non-polymers2,1758
Water6,521362
1
A: Iron-chelator utilization protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7876
Polymers30,5811
Non-polymers1,2055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Iron-chelator utilization protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5504
Polymers30,5811
Non-polymers9693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.541, 75.067, 73.904
Angle α, β, γ (deg.)90.00, 102.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Iron-chelator utilization protein


Mass: 30581.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca TM51 (bacteria) / Gene: TM51_09581 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: R9F6K7, UniProt: A0A0M3KL21*PLUS
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 55.2 % / Description: cuboid
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.95 M ammonia sulfate, 0.1 M Tris-HCl pH 6.6 and 35% v/v 2-methyl-2, 4-pentanediol
PH range: 6.4 - 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.889→37.53 Å / Num. obs: 54927 / % possible obs: 99.28 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.05742 / Rsym value: 0.06708 / Net I/σ(I): 13.3
Reflection shellResolution: 1.889→1.957 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.64 / % possible all: 94.18

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDS10.5.8data reduction
Coot0.7model building
PHASER2.1.2phasing
Aimless0.5.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GPJ

2gpj


Resolution: 1.8892→36.744 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 2764 5.06 %Random selection
Rwork0.1888 ---
obs0.1903 54668 98.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8892→36.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4141 0 140 362 4643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074383
X-RAY DIFFRACTIONf_angle_d1.3035983
X-RAY DIFFRACTIONf_dihedral_angle_d14.5421587
X-RAY DIFFRACTIONf_chiral_restr0.04644
X-RAY DIFFRACTIONf_plane_restr0.005776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8892-1.92180.46241420.44872270X-RAY DIFFRACTION87
1.9218-1.95670.38981200.33722593X-RAY DIFFRACTION99
1.9567-1.99430.27711340.22842632X-RAY DIFFRACTION100
1.9943-2.0350.22421110.20742648X-RAY DIFFRACTION100
2.035-2.07930.26151580.20052595X-RAY DIFFRACTION100
2.0793-2.12770.23491550.19782600X-RAY DIFFRACTION100
2.1277-2.18090.22521370.20672626X-RAY DIFFRACTION100
2.1809-2.23980.28961450.24172544X-RAY DIFFRACTION97
2.2398-2.30570.33381210.28092513X-RAY DIFFRACTION96
2.3057-2.38010.23081480.20122603X-RAY DIFFRACTION100
2.3801-2.46520.24121420.19772618X-RAY DIFFRACTION100
2.4652-2.56390.2471560.19632625X-RAY DIFFRACTION100
2.5639-2.68050.27931400.19642634X-RAY DIFFRACTION100
2.6805-2.82180.2391400.19782608X-RAY DIFFRACTION100
2.8218-2.99850.22451320.19972651X-RAY DIFFRACTION99
2.9985-3.22990.21391410.18852600X-RAY DIFFRACTION100
3.2299-3.55470.18031300.16852647X-RAY DIFFRACTION99
3.5547-4.06850.17531190.15182614X-RAY DIFFRACTION98
4.0685-5.12370.15521630.14172586X-RAY DIFFRACTION98
5.1237-36.75050.19081300.1652697X-RAY DIFFRACTION98

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