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- PDB-5d1x: IsdB NEAT2 bound by D4-30 -

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Basic information

Entry
Database: PDB / ID: 5d1x
TitleIsdB NEAT2 bound by D4-30
Components
  • D4-30 Heavy Chain
  • D4-30 Light Chain
  • Iron-regulated surface determinant protein B
  • P5 Heavy Chain
  • P5 Light Chain
KeywordsIMMUNE SYSTEM / IsdB / NEAT2 / germline encoded
Function / homology
Function and homology information


heme transmembrane transporter activity / extracellular region / metal ion binding
Similarity search - Function
Iron-regulated surface determinant protein IsdB / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / : ...Iron-regulated surface determinant protein IsdB / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / 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 / Iron-regulated surface determinant protein B
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsDeng, X.
CitationJournal: Nat Commun / Year: 2016
Title: Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire.
Authors: Yeung, Y.A. / Foletti, D. / Deng, X. / Abdiche, Y. / Strop, P. / Glanville, J. / Pitts, S. / Lindquist, K. / Sundar, P.D. / Sirota, M. / Hasa-Moreno, A. / Pham, A. / Melton Witt, J. / Ni, I. ...Authors: Yeung, Y.A. / Foletti, D. / Deng, X. / Abdiche, Y. / Strop, P. / Glanville, J. / Pitts, S. / Lindquist, K. / Sundar, P.D. / Sirota, M. / Hasa-Moreno, A. / Pham, A. / Melton Witt, J. / Ni, I. / Pons, J. / Shelton, D. / Rajpal, A. / Chaparro-Riggers, J.
History
DepositionAug 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D4-30 Light Chain
B: D4-30 Heavy Chain
C: P5 Heavy Chain
D: P5 Light Chain
E: Iron-regulated surface determinant protein B


Theoretical massNumber of molelcules
Total (without water)118,8095
Polymers118,8095
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-53 kcal/mol
Surface area44600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.251, 111.251, 105.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Antibody D4-30 Light Chain


Mass: 24085.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody D4-30 Heavy Chain


Mass: 27757.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody P5 Heavy Chain


Mass: 29434.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody P5 Light Chain


Mass: 23651.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Protein Iron-regulated surface determinant protein B / Fur-regulated protein B / Staphylococcal iron-regulated protein H / Staphylococcus aureus surface protein J


Mass: 13879.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria)
Strain: USA300 / Gene: isdB, frpB, sasJ, sirH, SAUSA300_1028 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q2FHV2, UniProt: Q2FZF0*PLUS
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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 290 K / Method: microbatch / Details: 15% PEG10k 0.1M Tris pH 8

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.21→49.79 Å / % possible obs: 99 % / Redundancy: 3.6 % / Net I/σ(I): 9.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
SCALAdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.21→49.18 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.887 / SU B: 74.469 / SU ML: 0.545 / Cross valid method: THROUGHOUT / ESU R Free: 0.594
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30996 1208 5.8 %RANDOM
Rwork0.26903 ---
obs0.27138 19661 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.022 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 3.21→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6684 0 0 0 6684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196839
X-RAY DIFFRACTIONr_bond_other_d0.0020.026311
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9459287
X-RAY DIFFRACTIONr_angle_other_deg0.998314576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7575861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25723.791277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.242151114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8321535
X-RAY DIFFRACTIONr_chiral_restr0.0880.21052
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217675
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021546
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_it0.1934.4273468
X-RAY DIFFRACTIONr_mcbond_other0.1934.4273467
X-RAY DIFFRACTIONr_mcangle_it0.3226.6394321
X-RAY DIFFRACTIONr_mcangle_other0.3226.6394322
X-RAY DIFFRACTIONr_scbond_it0.1734.4233371
X-RAY DIFFRACTIONr_scbond_other0.1734.4233372
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.2826.6364967
X-RAY DIFFRACTIONr_long_range_B_refined0.46834.4657053
X-RAY DIFFRACTIONr_long_range_B_other0.46834.4667054
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.21→3.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 98 -
Rwork0.323 1360 -
obs--93.88 %

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