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- PDB-5d1q: IsdB NEAT2 bound by clone D2-06 -

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Basic information

Entry
Database: PDB / ID: 5d1q
TitleIsdB NEAT2 bound by clone D2-06
Components
  • D2-06 Heavy Chain
  • D2-06 Light Chain
  • Iron-regulated surface determinant protein B
  • P5 Heavy Chain
  • P5 Light Chain
KeywordsIMMUNE SYSTEM / IsdB NEAT2 / IGVH1-69 / 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: 3.22 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 30, 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: D2-06 Light Chain
B: D2-06 Heavy Chain
C: P5 Heavy Chain
D: P5 Light Chain
E: Iron-regulated surface determinant protein B


Theoretical massNumber of molelcules
Total (without water)118,2025
Polymers118,2025
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint-60 kcal/mol
Surface area45230 Å2
Unit cell
Length a, b, c (Å)121.387, 121.387, 193.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Antibody D2-06 Light Chain


Mass: 23386.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cloned from B Cells / Source: (gene. exp.) Homo sapiens (human) / Cell: Memory B Cell / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody D2-06 Heavy Chain


Mass: 27782.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / 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) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: Antibody P5 Light Chain


Mass: 23564.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / 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: 14034.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
Strain: bovine RF122 / ET3-1 / Gene: isdB, frpB, sasJ, sirH, SAB0993c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q2YX96, 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: 3.27 Å3/Da / Density % sol: 62.35 % / Description: Plates
Crystal growTemperature: 293 K / Method: microbatch / Details: 20% PEG3350 0.1M Na Citrate pH 5.4 / PH range: 5.5-6

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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: 3.22→47.33 Å / Num. obs: 22680 / % possible obs: 98.8 % / Redundancy: 6.6 % / Net I/σ(I): 20.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
Cootmodel building
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.22→47.33 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.867 / SU B: 57.898 / SU ML: 0.422 / Cross valid method: THROUGHOUT / ESU R Free: 0.548
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28838 1242 5.2 %RANDOM
Rwork0.23872 ---
obs0.24118 22680 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.971 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0 Å2
2--0.06 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 3.22→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7575 0 0 0 7575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.027757
X-RAY DIFFRACTIONr_bond_other_d0.0070.027165
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.94810536
X-RAY DIFFRACTIONr_angle_other_deg0.972316586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.3965986
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29724.323303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.547151270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5431532
X-RAY DIFFRACTIONr_chiral_restr0.0850.21198
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218726
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021718
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_it043968
X-RAY DIFFRACTIONr_mcbond_other043967
X-RAY DIFFRACTIONr_mcangle_it064946
X-RAY DIFFRACTIONr_mcangle_other064947
X-RAY DIFFRACTIONr_scbond_it043789
X-RAY DIFFRACTIONr_scbond_other043790
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other065591
X-RAY DIFFRACTIONr_long_range_B_refined031.2278069
X-RAY DIFFRACTIONr_long_range_B_other031.2288070
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.216→3.299 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 100 -
Rwork0.314 1588 -
obs--96.13 %
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)
13.0227-1.74390.31031.98610.96072.47990.28980.1383-0.0986-0.28160.0123-0.33940.2278-0.1366-0.30210.1393-0.0730.08680.1528-0.04410.20426.4203-48.1882-72.6299
21.4409-0.7585-0.00463.88731.33193.11150.0449-0.0363-0.3483-0.2162-0.03320.2280.2198-0.6854-0.01170.1192-0.2204-0.04830.49460.10910.1299.2709-50.494-77.6112
30.7709-0.3125-0.10342.2946-2.12122.821-0.1561-0.0974-0.15360.19080.07-0.32580.18460.19210.08610.18820.0612-0.13130.239-0.10360.2604-10.6537-38.0537-16.9259
40.76190.09470.0174.1144-1.39313.1699-0.086-0.1206-0.4818-0.26070.170.07950.9586-0.6026-0.0840.3098-0.16070.0330.30650.02660.3312-20.631-45.6494-29.6139
52.5643-1.2088-1.5972.71390.88586.12090.24160.32340.2045-0.33-0.16140.2222-0.3070.0606-0.08020.0561-0.0042-0.03340.15940.09390.2701-9.6765-11.2706-56.5873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 214
2X-RAY DIFFRACTION2B1 - 220
3X-RAY DIFFRACTION3C1 - 217
4X-RAY DIFFRACTION4D1 - 212
5X-RAY DIFFRACTION5E339 - 456

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