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- PDB-3okk: Crystal structure of S25-39 in complex with Kdo(2.4)Kdo -

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Basic information

Entry
Database: PDB / ID: 3okk
TitleCrystal structure of S25-39 in complex with Kdo(2.4)Kdo
Components
  • S25-39 Fab (IgG1k) heavy chain
  • S25-39 Fab (IgG1k) light chain
KeywordsIMMUNE SYSTEM / antibody / Fab / IgG / carbohydrate
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsBlackler, R.J. / Evans, S.V.
CitationJournal: Biochemistry / Year: 2011
Title: A Common NH53K Mutation in the Combining Site of Antibodies Raised against Chlamydial LPS Glycoconjugates Significantly Increases Avidity.
Authors: Blackler, R.J. / Brooks, C.L. / Evans, D.W. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V.
History
DepositionAug 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_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.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S25-39 Fab (IgG1k) light chain
B: S25-39 Fab (IgG1k) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9205
Polymers48,2912
Non-polymers6293
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-44 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.628, 81.441, 131.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody S25-39 Fab (IgG1k) light chain


Mass: 24267.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#2: Antibody S25-39 Fab (IgG1k) heavy chain


Mass: 24022.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#3: Polysaccharide 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2- ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid


Type: oligosaccharide / Mass: 498.433 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[Aad1122h-2a_2-6_2*OCC=C][Aad1122h-2a_2-6]/1-2/a4-b2WURCSPDB2Glycan 1.1.0
[][propyl]{[(1+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THERE WAS EXTRA ELECTRON DENSITY OBSERVED AT THE END OF THE LIGHT CHAIN IN ...AUTHORS STATE THAT THERE WAS EXTRA ELECTRON DENSITY OBSERVED AT THE END OF THE LIGHT CHAIN IN ADDITION TO THE KNOWN SEQUENCE FOR THIS FAB. AN UNK HAS BEEN MODELLED HERE TO REPRESENT THE UNKNOWN RESIDUE.

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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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 289 K / Method: hanging drop / pH: 6.5
Details: PEG 3350, MPD, ZnAc, NaCacod, pH 6.5, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 11, 2010 / Details: OSMIC BLUE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→19.9 Å / Num. obs: 35350 / % possible obs: 96.7 % / Redundancy: 3.35 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obs% possible all
1.95-2.023.480.2893.495.8
2.02-2.13.450.2393.795.7
2.1-2.23.430.1944.496.2
2.2-2.313.370.1575.396.7
2.31-2.463.350.1256.496
2.46-2.653.280.0967.895.9
2.65-2.913.210.06910.895.1
2.91-3.333.180.04815.296.5
3.33-4.193.30.03322.699.1
4.19-19.93.490.02928.499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 33.2 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.9 Å
Translation2.5 Å19.9 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.7 W8RSSIdata scaling
PHASER2.1.4phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.765 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.32 / σ(F): 1.33 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 1772 5.01 %
Rwork0.1951 --
obs0.1971 35338 96.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.431 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3555 Å20 Å2-0 Å2
2--0.8572 Å2-0 Å2
3----0.5017 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3344 0 36 396 3776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053504
X-RAY DIFFRACTIONf_angle_d0.9814775
X-RAY DIFFRACTIONf_dihedral_angle_d12.0611270
X-RAY DIFFRACTIONf_chiral_restr0.063542
X-RAY DIFFRACTIONf_plane_restr0.003605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00270.33931290.26852527X-RAY DIFFRACTION96
2.0027-2.06160.30191350.24112508X-RAY DIFFRACTION96
2.0616-2.1280.28441250.23072520X-RAY DIFFRACTION96
2.128-2.2040.29121450.24252530X-RAY DIFFRACTION96
2.204-2.29210.31071290.23582556X-RAY DIFFRACTION97
2.2921-2.39630.28461230.22952565X-RAY DIFFRACTION96
2.3963-2.52240.29231250.22592551X-RAY DIFFRACTION96
2.5224-2.680.30951580.22162528X-RAY DIFFRACTION96
2.68-2.88640.23171310.21042516X-RAY DIFFRACTION95
2.8864-3.17580.24931400.20142565X-RAY DIFFRACTION96
3.1758-3.63280.21731410.18552638X-RAY DIFFRACTION98
3.6328-4.56770.18461540.15652720X-RAY DIFFRACTION99
4.5677-19.76620.19631370.17352842X-RAY DIFFRACTION99

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