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- PDB-7xli: Crystal structure of IsdB linker-NEAT2 bound to a nanobody (VHH) -

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Basic information

Entry
Database: PDB / ID: 7xli
TitleCrystal structure of IsdB linker-NEAT2 bound to a nanobody (VHH)
Components
  • Iron-regulated surface determinant protein B
  • VHH6 nanobody
KeywordsMETAL TRANSPORT / IsdH system Heme Staphylococcus aureus VHH Nanodoby Antimicrobial
Function / homology
Function and homology information


heme transmembrane transporter activity / metal ion binding / membrane
Similarity search - Function
Iron-regulated surface determinant protein IsdB / : / Iron-regulated surface determinant protein H/B, linker domain / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / : / YSIRK type signal peptide ...Iron-regulated surface determinant protein IsdB / : / Iron-regulated surface determinant protein H/B, linker domain / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / : / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Iron-regulated surface determinant protein B
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCaaveiro, J.M.M. / Valenciano-Bellido, S. / Tsumoto, K.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H05766 Japan
Japan Society for the Promotion of Science (JSPS)20H02531 Japan
Japan Agency for Medical Research and Development (AMED)JP19fk0108073h Japan
Japan Agency for Medical Research and Development (AMED)JP18fm0208030h Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101094 Japan
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth.
Authors: Valenciano-Bellido, S. / Caaveiro, J.M.M. / Nakakido, M. / Kuroda, D. / Aikawa, C. / Nakagawa, I. / Tsumoto, K.
History
DepositionApr 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Mar 6, 2024Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron-regulated surface determinant protein B
B: VHH6 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2204
Polymers36,1452
Non-polymers762
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-28 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.321, 48.580, 140.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Iron-regulated surface determinant protein B / Fur-regulated protein B / Staphylococcal iron-regulated protein H / Staphylococcus aureus surface protein J


Mass: 21177.322 Da / Num. of mol.: 1 / Fragment: NEAT2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: isdB, C7M54_06565, DD547_01151, EP54_07185, EQ90_05325, FAF17_11720, GO814_06830, GO942_06780, GQX37_07535, NCTC13131_00513, SA950122_02636, SAHC1335_02047, SAMEA103891415_00297, SAMEA2076235_ ...Gene: isdB, C7M54_06565, DD547_01151, EP54_07185, EQ90_05325, FAF17_11720, GO814_06830, GO942_06780, GQX37_07535, NCTC13131_00513, SA950122_02636, SAHC1335_02047, SAMEA103891415_00297, SAMEA2076235_00033, SAMEA2078260_00343, SAMEA2078588_00277, SAMEA2078837_01385, SAMEA2080344_00033, SAMEA2081063_00033, SAMEA4008575_00033, SAMEA70146418_01784
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6HSN6
#2: Protein VHH6 nanobody


Mass: 14967.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.96 Å3/Da / Density % sol: 37.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG 3,350 0.1 M HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 31303 / % possible obs: 99.8 % / Redundancy: 8.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.025 / Net I/σ(I): 14.7
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.828 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4429 / CC1/2: 0.827 / Rpim(I) all: 0.325

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XLD

7xld


Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.417 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 1251 4 %RANDOM
Rwork0.2088 ---
obs0.21 29982 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.02 Å2 / Biso mean: 42.314 Å2 / Biso min: 20.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2--0.33 Å20 Å2
3----2.26 Å2
Refinement stepCycle: final / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 2 111 2001
Biso mean--46.72 38.97 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131948
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171755
X-RAY DIFFRACTIONr_angle_refined_deg1.781.6492634
X-RAY DIFFRACTIONr_angle_other_deg1.3911.5874078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.5445.145242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24223.302106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4415344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.751159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022292
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02422
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 82 -
Rwork0.298 2158 -
all-2240 -
obs--97.26 %
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)
11.52390.44840.94381.6921.30014.84380.09870.4894-0.4611-0.3439-0.05040.2350.3574-0.4523-0.04830.3209-0.0165-0.07580.4035-0.09930.3822-3.68855.14065.458
21.34980.1023-0.46952.444-0.25442.8567-0.0006-0.07820.0010.23510.0194-0.09360.06730.2227-0.01870.1281-0.0008-0.02270.0204-0.0030.15254.167612.480433.9734
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A342 - 451
2X-RAY DIFFRACTION2B1 - 125

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