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- PDB-1q9k: S25-2 Fab Unliganded 1 -

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Basic information

Entry
Database: PDB / ID: 1q9k
TitleS25-2 Fab Unliganded 1
Components
  • S25-2 Fab (IgG1k) heavy chain
  • S25-2 Fab (IgG1k) light chain
KeywordsIMMUNE SYSTEM / antigen-binding fragment / Fab / anti-carbohydrate / anti-LPS / antibody / immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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_seq_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_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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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
A: S25-2 Fab (IgG1k) light chain
B: S25-2 Fab (IgG1k) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4516
Polymers48,3542
Non-polymers974
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-51 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.800, 112.200, 41.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody S25-2 Fab (IgG1k) light chain


Mass: 24242.898 Da / Num. of mol.: 1 / Fragment: Light Chain kappa / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody S25-2 Fab (IgG1k) heavy chain


Mass: 24110.967 Da / Num. of mol.: 1 / Fragment: Heavy Chain g1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#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


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: zinc acetate, magnesium chloride, PEG 4000, PEG 8000, cacodylate, tris, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
118 mg/mlFab1drop
240 mM1dropMgCl2
330 mM1dropZnCl2
48 %(w/v)PEG40001drop
511 %(w/v)ethylene glycol1drop
620 mMTris1droppH8
7200 mM1reservoirMgCl2
825 %(w/v)PEG40001reservoir
9100 mMTris1reservoirpH8.5

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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: Mar 22, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 1.96→19.74 Å / Num. all: 31806 / Num. obs: 29982 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.1 Å2 / Limit h max: 48 / Limit h min: 0 / Limit k max: 56 / Limit k min: 0 / Limit l max: 20 / Limit l min: 0 / Observed criterion F max: 244216.73 / Observed criterion F min: 0.32
Reflection shellResolution: 1.96→2.03 Å / % possible all: 87.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 31827 / % possible obs: 96.1 % / Num. measured all: 203789 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 87.5 % / Num. unique obs: 2827 / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q9O, S45-18 Fab unliganded

1q9o


Resolution: 1.96→19.74 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2995 10 %random
Rwork0.228 ---
all-33200 --
obs-29982 90.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 67.8721 Å2 / ksol: 0.348868 e/Å3
Displacement parametersBiso max: 99.54 Å2 / Biso mean: 40.2 Å2 / Biso min: 18.64 Å2
Baniso -1Baniso -2Baniso -3
1--8.76 Å20 Å20 Å2
2---8.84 Å20 Å2
3---17.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.34 Å
Luzzati d res high-1.96
Refinement stepCycle: LAST / Resolution: 1.96→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3399 0 4 269 3672
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_torsion_deg27.3
X-RAY DIFFRACTIONc_torsion_impr_deg0.95
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 (%)
1.96-2.030.34425410.60.32121400.0223248239473.7
2.03-2.110.3762659.60.31524850.0233288275083.6
2.11-2.210.35426690.28826820.0223291294889.6
2.21-2.330.37229310.80.31824290.0223286272282.8
2.33-2.470.30830810.20.24527250.0183276303392.6
2.47-2.660.323049.90.24827600.0183286306493.2
2.66-2.930.33532810.30.24628450.0193323317395.5
2.93-3.350.27325100.21629130.0153333323897.1
3.35-4.210.24533810.30.19629530.0133390329197.1
4.21-19.740.2253149.30.20430550.0133518336995.8
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.paramwater.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.01

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