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- PDB-1q9o: S45-18 Fab Unliganded -

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Basic information

Entry
Database: PDB / ID: 1q9o
TitleS45-18 Fab Unliganded
Components
  • S45-2 Fab (IgG1k) heavy chain
  • S45-2 Fab (IgG1k) light chain
KeywordsIMMUNE SYSTEM / antigen-binding fragment / Fab / anti-carbohydrate / anti-LPS / antibody / immunoglobulin
Function / homology
Function and homology information


IgG immunoglobulin complex / B cell differentiation / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Igh protein / Immunoglobulin kappa constant
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsNguyen, H.P. / Seto, N.O. / MacKenzie, C.R. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Germline antibody recognition of distinct carbohydrate epitopes.
Authors: Nguyen, H.P. / Seto, N.O. / MacKenzie, C.R. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V.
History
DepositionAug 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The sequence of the protein was not deposited into any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: S45-2 Fab (IgG1k) heavy chain
D: S45-2 Fab (IgG1k) heavy chain
A: S45-2 Fab (IgG1k) light chain
C: S45-2 Fab (IgG1k) light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6008
Polymers97,5034
Non-polymers974
Water9,458525
1
B: S45-2 Fab (IgG1k) heavy chain
A: S45-2 Fab (IgG1k) light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8004
Polymers48,7512
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-46 kcal/mol
Surface area20090 Å2
MethodPISA
2
D: S45-2 Fab (IgG1k) heavy chain
C: S45-2 Fab (IgG1k) light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8004
Polymers48,7512
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-36 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.400, 170.300, 77.100
Angle α, β, γ (deg.)90.00, 114.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody S45-2 Fab (IgG1k) heavy chain


Mass: 24445.398 Da / Num. of mol.: 2 / Fragment: Fab1 Heavy chain g1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: I6L985*PLUS
#2: Antibody S45-2 Fab (IgG1k) light chain


Mass: 24306.039 Da / Num. of mol.: 2 / Fragment: Fab1 Light chain kappa / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837*PLUS
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: potassium phosphate, PEG 8000, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: Nguyen, H.P., (2001) Acta Cryst., D57, 1872.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16-8 mg/mlFab1drop
210 %(w/v)PEG80001drop
325 mM1droppH7.8K3PO4
420 %(w/v)PEG80001reservoir
550 mM1reservoirpH7.8K3PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.15 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2002 / Details: mirrors
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 1.79→19.18 Å / Num. all: 75932 / Num. obs: 74454 / % possible obs: 88.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.1 Å2 / Limit h max: 38 / Limit h min: -42 / Limit k max: 95 / Limit k min: -42 / Limit l max: 43 / Limit l min: 0 / Observed criterion F max: 240848.79 / Observed criterion F min: 0.32
Reflection shellResolution: 1.79→1.85 Å / % possible all: 78.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 75932 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Num. measured all: 234850 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 78.5 % / Num. unique obs: 6553 / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 6.9

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fv domain of YST 9.1 Fab unliganded (PDB entry 1MAM)

1mam


Resolution: 1.79→19.18 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 7500 10.1 %random
Rwork0.22 ---
all-84009 --
obs-74454 88.6 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 43.4159 Å2 / ksol: 0.327425 e/Å3
Displacement parametersBiso max: 84.92 Å2 / Biso mean: 30.11 Å2 / Biso min: 14.35 Å2
Baniso -1Baniso -2Baniso -3
1--3.31 Å20 Å2-2.17 Å2
2--3.36 Å20 Å2
3----0.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.14 Å
Luzzati d res high-1.79
Refinement stepCycle: LAST / Resolution: 1.79→19.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6850 0 4 525 7379
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_torsion_deg26.9
X-RAY DIFFRACTIONc_torsion_impr_deg0.81
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.79-1.850.30963110.20.26255430.0128380617473.7
1.85-1.930.3276419.90.28558480.0138414648977.1
1.93-2.020.297599.90.24469070.0118420766691
2.02-2.120.29684010.50.23671390.018410797994.9
2.12-2.250.274673100.23160740.0118388674780.4
2.25-2.430.2935759.70.24853710.0128364594671.1
2.43-2.670.2968059.70.24374620.018431826798.1
2.67-3.060.28384310.10.24575230.018422836699.3
3.06-3.850.2298339.90.22575510.0088407838499.7
3.85-19.180.1990010.70.17275360.0068484843699.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.007

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