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- PDB-6m87: Fab 10A6 in complex with MPTS -

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Basic information

Entry
Database: PDB / ID: 6m87
TitleFab 10A6 in complex with MPTS
Components
  • Fab 10A6 heavy chain
  • Fab 10A6 light chain
KeywordsIMMUNE SYSTEM / antibody dynamics
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 8-methoxypyrene-1,3,6-trisulfonic acid
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.609 Å
AuthorsStanfield, R.L. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI079319 United States
CitationJournal: Biochemistry / Year: 2019
Title: Structure and Dynamics of Stacking Interactions in an Antibody Binding Site.
Authors: Adhikary, R. / Zimmermann, J. / Stanfield, R.L. / Wilson, I.A. / Yu, W. / Oda, M. / Romesberg, F.E.
History
DepositionAug 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Dec 18, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 2.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Fab 10A6 light chain
B: Fab 10A6 heavy chain
C: Fab 10A6 light chain
E: Fab 10A6 light chain
G: Fab 10A6 light chain
I: Fab 10A6 light chain
K: Fab 10A6 light chain
D: Fab 10A6 heavy chain
F: Fab 10A6 heavy chain
H: Fab 10A6 heavy chain
J: Fab 10A6 heavy chain
L: Fab 10A6 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,68124
Polymers278,27012
Non-polymers3,41112
Water2,666148
1
A: Fab 10A6 light chain
B: Fab 10A6 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9474
Polymers46,3782
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-37 kcal/mol
Surface area19560 Å2
MethodPISA
2
C: Fab 10A6 light chain
D: Fab 10A6 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9474
Polymers46,3782
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-37 kcal/mol
Surface area19700 Å2
MethodPISA
3
E: Fab 10A6 light chain
F: Fab 10A6 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9474
Polymers46,3782
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-36 kcal/mol
Surface area19530 Å2
MethodPISA
4
G: Fab 10A6 light chain
H: Fab 10A6 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9474
Polymers46,3782
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-37 kcal/mol
Surface area19440 Å2
MethodPISA
5
I: Fab 10A6 light chain
J: Fab 10A6 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9474
Polymers46,3782
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-37 kcal/mol
Surface area19650 Å2
MethodPISA
6
K: Fab 10A6 light chain
L: Fab 10A6 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9474
Polymers46,3782
Non-polymers5692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-37 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.485, 186.485, 89.909
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Antibody
Fab 10A6 light chain


Mass: 23113.496 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody
Fab 10A6 heavy chain


Mass: 23264.797 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical
ChemComp-2M9 / 8-methoxypyrene-1,3,6-trisulfonic acid


Mass: 472.466 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H12O10S3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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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: 3.26 Å3/Da / Density % sol: 62.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 1.6M ammonium sulfate, 0.1M acetate, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.6→44.8 Å / Num. obs: 106209 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 60 Å2 / CC1/2: 0.879 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.045 / Rrim(I) all: 0.108 / Net I/av σ(I): 20 / Net I/σ(I): 20
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.97 / Mean I/σ(I) obs: 1 / Num. unique obs: 5329 / CC1/2: 0.384 / Rpim(I) all: 0.91 / Rrim(I) all: 2.16 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MEX

1mex


Resolution: 2.609→44.792 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 85.79 / Phase error: 33.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 5164 4.86 %RANDOM
Rwork0.2275 ---
obs0.243 106174 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.609→44.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19358 0 210 148 19716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00220087
X-RAY DIFFRACTIONf_angle_d0.61327460
X-RAY DIFFRACTIONf_dihedral_angle_d8.86912024
X-RAY DIFFRACTIONf_chiral_restr0.0443073
X-RAY DIFFRACTIONf_plane_restr0.0043638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6086-2.65360.3492760.33164820X-RAY DIFFRACTION90
2.6536-2.70180.34592740.33075066X-RAY DIFFRACTION95
2.7018-2.75380.36472320.33365079X-RAY DIFFRACTION96
2.7538-2.810.40442500.32045042X-RAY DIFFRACTION95
2.81-2.8710.42500.31555100X-RAY DIFFRACTION95
2.871-2.93780.33682640.31615021X-RAY DIFFRACTION95
2.9378-3.01130.39292360.31915117X-RAY DIFFRACTION96
3.0113-3.09270.33672260.31375125X-RAY DIFFRACTION96
3.0927-3.18360.32322780.29525007X-RAY DIFFRACTION95
3.1836-3.28640.32843020.28415058X-RAY DIFFRACTION94
3.2864-3.40380.30572540.28285036X-RAY DIFFRACTION95
3.4038-3.540.3512440.27985048X-RAY DIFFRACTION95
3.54-3.7010.31072940.26235082X-RAY DIFFRACTION95
3.701-3.8960.31062280.24945094X-RAY DIFFRACTION96
3.896-4.140.27942660.23035059X-RAY DIFFRACTION95
4.14-4.45930.27122400.19455072X-RAY DIFFRACTION95
4.4593-4.90750.19932840.18175040X-RAY DIFFRACTION95
4.9075-5.61630.23692720.18575063X-RAY DIFFRACTION95
5.6163-7.0710.24842460.20675042X-RAY DIFFRACTION95
7.071-43.3140.2182360.2245049X-RAY DIFFRACTION95

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