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- PDB-5d1z: IsdB NEAT1 bound by clone D4-10 -

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Basic information

Entry
Database: PDB / ID: 5d1z
TitleIsdB NEAT1 bound by clone D4-10
Components
  • D4-10 Heavy Chain
  • D4-10 Light Chain
  • Iron-regulated surface determinant protein B
  • Y10 Heavy Chain
  • Y10 Light Chain
KeywordsIMMUNE SYSTEM / IsdB / NEAT1 / germline encoded
Function / homology
Function and homology information


heme transmembrane transporter activity / protein phosphatase regulator activity / regulation of mitotic nuclear division / chromosome segregation / chromosome / cell division / extracellular region / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Protein phosphatase 1 binding domain / Protein phosphatase 1 binding / Iron-regulated surface determinant protein IsdB / Immunoglobulin-like - #1850 / : / Iron-regulated surface determinant protein H/B, linker domain / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain ...Protein phosphatase 1 binding domain / Protein phosphatase 1 binding / Iron-regulated surface determinant protein IsdB / Immunoglobulin-like - #1850 / : / 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
Cell division cycle-associated protein 2 / Iron-regulated surface determinant protein B
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 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 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Nov 20, 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: Y10 Light Chain
B: Y10 Heavy Chain
C: D4-10 Light Chain
D: D4-10 Heavy Chain
I: Iron-regulated surface determinant protein B
E: D4-10 Light Chain
F: D4-10 Heavy Chain
G: Y10 Heavy Chain
H: Y10 Light Chain
J: Iron-regulated surface determinant protein B


Theoretical massNumber of molelcules
Total (without water)245,42410
Polymers245,42410
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23190 Å2
ΔGint-116 kcal/mol
Surface area87740 Å2
2
A: Y10 Light Chain
B: Y10 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)52,0222
Polymers52,0222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-22 kcal/mol
Surface area19720 Å2
MethodPISA
3
C: D4-10 Light Chain
D: D4-10 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)52,5762
Polymers52,5762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-22 kcal/mol
Surface area20080 Å2
MethodPISA
4
E: D4-10 Light Chain
F: D4-10 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)52,5762
Polymers52,5762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-22 kcal/mol
Surface area19730 Å2
MethodPISA
5
G: Y10 Heavy Chain
H: Y10 Light Chain


Theoretical massNumber of molelcules
Total (without water)52,0222
Polymers52,0222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-28 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.292, 147.005, 165.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Antibody Y10 Light Chain


Mass: 23466.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Y10 Heavy Chain


Mass: 28555.459 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody D4-10 Light Chain


Mass: 23341.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody D4-10 Heavy Chain


Mass: 29234.268 Da / Num. of mol.: 2
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: 18114.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain MSSA476) (bacteria)
Strain: MSSA476 / Gene: isdB, frpB, sasJ, sirH, SAS1063 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q6GA86, UniProt: Q69YH5*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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 290 K / Method: microbatch / Details: 17% PEG 3350 0.2M Ammonium Citrate Tri

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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: 3.17→24.96 Å / Num. obs: 45212 / % possible obs: 97.9 % / Redundancy: 3.5 % / Net I/σ(I): 7.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.17→24.96 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.844 / SU B: 60.916 / SU ML: 0.433 / 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
Rfree0.28712 2344 4.9 %RANDOM
Rwork0.23342 ---
obs0.23605 45211 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.053 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å20 Å2
2--0.5 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 3.17→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15704 0 0 0 15704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0216095
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214818
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.94821854
X-RAY DIFFRACTIONr_angle_other_deg1.105334296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.01752025
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92124.32662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.788152605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1971570
X-RAY DIFFRACTIONr_chiral_restr0.1040.22425
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02118145
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023641
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_it0.8913.1038142
X-RAY DIFFRACTIONr_mcbond_other0.8913.1038141
X-RAY DIFFRACTIONr_mcangle_it1.5944.65110153
X-RAY DIFFRACTIONr_mcangle_other1.5944.65110154
X-RAY DIFFRACTIONr_scbond_it0.6493.0497953
X-RAY DIFFRACTIONr_scbond_other0.6493.057954
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2044.5911702
X-RAY DIFFRACTIONr_long_range_B_refined2.58623.0915304
X-RAY DIFFRACTIONr_long_range_B_other2.58523.09215305
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.165→3.246 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 179 -
Rwork0.339 2967 -
obs--90.27 %
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)
10.5662-0.2214-0.86610.23940.39371.3905-0.1285-0.181-0.00920.17210.06280.17230.21850.21120.06560.21420.02950.0380.15950.04520.3164-118.034-24.277-25.1962
20.5334-0.4403-0.47120.73810.5480.64640.16-0.00630.1553-0.0888-0.09260.0449-0.2056-0.1206-0.06750.13330.0010.00820.091500.2183-116.8415-16.7056-41.707
31.6427-0.95330.64741.42480.02570.62190.0398-0.2283-0.21730.14790.03870.02910.2144-0.1191-0.07850.1099-0.01330.00460.05360.0210.0965-58.0129-84.7469-23.4395
41.1302-0.88590.70790.9389-0.37181.2326-0.0918-0.4905-0.20210.30040.33370.13260.1497-0.2967-0.24180.2074-0.0075-0.00890.23780.07130.1378-74.9347-76.7297-22.8551
51.8765-0.51130.30731.1875-0.22280.06970.00920.3740.0764-0.3291-0.081-0.08780.03960.06810.07180.10950.00040.02070.09370.05720.0954-81.5441-48.3105-54.0896
61.52690.0549-0.54820.2092-0.28220.5560.0385-0.37690.16280.2092-0.022-0.0062-0.3050.0848-0.01640.22190.0134-0.05260.1636-0.01270.2515-114.134737.5804-12.6571
70.5636-0.0839-0.24340.38310.2341.1757-0.0152-0.4380.05020.20870.1154-0.1141-0.2140.3352-0.10020.23010.0015-0.03980.3694-0.01810.2155-97.500428.6527-13.2072
80.010.0269-0.01960.8089-0.39320.3060.0352-0.0253-0.0305-0.0219-0.0918-0.01530.13660.0810.05660.1635-0.01420.00680.08940.03350.1682-56.2967-31.7558-32.859
90.1528-0.14220.40760.5503-0.65421.2887-0.0199-0.0603-0.01760.22770.0484-0.0952-0.1802-0.1184-0.02840.14290.01840.01950.1524-0.01810.2651-55.0642-25.544-15.6639
102.3475-0.9534-0.14041.13840.18520.03110.06460.3795-0.1136-0.2546-0.13240.1258-0.0416-0.02340.06780.08170.012-0.00540.06460.00240.181-91.43010.5147-43.6365
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 215
2X-RAY DIFFRACTION2B2 - 223
3X-RAY DIFFRACTION3C2 - 214
4X-RAY DIFFRACTION4D1 - 230
5X-RAY DIFFRACTION5I119 - 267
6X-RAY DIFFRACTION6E3 - 215
7X-RAY DIFFRACTION7F1 - 228
8X-RAY DIFFRACTION8G1 - 225
9X-RAY DIFFRACTION9H3 - 216
10X-RAY DIFFRACTION10J119 - 267

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