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- PDB-4m93: Unliganded 2 crystal structure of S25-26 Fab -

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Basic information

Entry
Database: PDB / ID: 4m93
TitleUnliganded 2 crystal structure of S25-26 Fab
Components(S25-26 Fab (IgG1k) ...) x 2
KeywordsIMMUNE SYSTEM / Carbohydrate/Sugar Binding
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsHaji-Ghassemi, O. / Evans, S.V.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Groove-type Recognition of Chlamydiaceae-specific Lipopolysaccharide Antigen by a Family of Antibodies Possessing an Unusual Variable Heavy Chain N-Linked Glycan.
Authors: Haji-Ghassemi, O. / Muller-Loennies, S. / Saldova, R. / Muniyappa, M. / Brade, L. / Rudd, P.M. / Harvey, D.J. / Kosma, P. / Brade, H. / Evans, S.V.
History
DepositionAug 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Jul 9, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.pdbx_role / _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
Revision 2.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
L: S25-26 Fab (IgG1k) light chain
H: S25-26 Fab (IgG1k) heavy chain
C: S25-26 Fab (IgG1k) light chain
B: S25-26 Fab (IgG1k) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,16810
Polymers95,5094
Non-polymers6606
Water4,900272
1
L: S25-26 Fab (IgG1k) light chain
H: S25-26 Fab (IgG1k) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9763
Polymers47,7542
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-25 kcal/mol
Surface area20020 Å2
MethodPISA
2
C: S25-26 Fab (IgG1k) light chain
B: S25-26 Fab (IgG1k) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1937
Polymers47,7542
Non-polymers4385
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-24 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.894, 88.806, 101.890
Angle α, β, γ (deg.)90.000, 102.060, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21C
12H
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010L1 - 218
2010C1 - 218
1020H1 - 218
2020B1 - 218

NCS ensembles :
ID
1
2

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Components

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Antibody , 2 types, 4 molecules LCHB

#1: Antibody S25-26 Fab (IgG1k) light chain


Mass: 24356.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/C
#2: Antibody S25-26 Fab (IgG1k) heavy chain


Mass: 23398.377 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/C

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Sugars , 1 types, 2 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 276 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES, 0.2M calcium acetate, 10% (V/V) isopropanol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2011 / Details: Vertical focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.09→25 Å / Num. obs: 61241 / % possible obs: 98.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.114 / Χ2: 1.017 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.09-2.162.90.57759880.846196.8
2.16-2.253.20.46560410.927197.3
2.25-2.353.30.38860740.947197.7
2.35-2.483.30.30460921.053197.8
2.48-2.633.30.21461051.069198
2.63-2.843.30.1561301.03198.2
2.84-3.123.30.10861331.127198.4
3.12-3.573.30.08761791.089198.8
3.57-4.493.30.0862091.001199
4.49-253.30.07662901.04198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.77 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.68 Å
Translation2.5 Å28.68 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MacromolecularCrystallography Data Collector (MxDC)data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4M7J

4m7j


Resolution: 2.09→24.87 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2743 / WRfactor Rwork: 0.2367 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8196 / SU B: 10.287 / SU ML: 0.141 / SU R Cruickshank DPI: 0.2244 / SU Rfree: 0.1861 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 3113 5.1 %RANDOM
Rwork0.2176 ---
obs0.2194 61241 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.63 Å2 / Biso mean: 38.3666 Å2 / Biso min: 16.23 Å2
Baniso -1Baniso -2Baniso -3
1--3.53 Å20 Å2-0.56 Å2
2--4.95 Å2-0 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.09→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6706 0 41 272 7019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026950
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9529498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8095874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13624270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.416151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6081528
X-RAY DIFFRACTIONr_chiral_restr0.0950.21067
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215254
X-RAY DIFFRACTIONr_mcbond_it0.9471.8263502
X-RAY DIFFRACTIONr_mcangle_it1.5482.7274372
X-RAY DIFFRACTIONr_scbond_it1.331.963448
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11L2840.12
12C2840.12
21H2690.13
22B2690.13
LS refinement shellResolution: 2.09→2.122 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 182 -
Rwork0.279 3483 -
all-3665 -
obs--78.58 %
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)
13.52431.29641.09262.9374-0.44159.4807-0.26960.42710.0655-0.15760.29720.11590.3434-0.6573-0.02760.1166-0.09440.03830.13070.00590.0682-31.36057.81240.8532
21.28662.82771.71328.07082.83772.97690.0644-0.0129-0.10220.27470.0642-0.1610.09370.0248-0.12860.09490.02340.0270.042-0.00170.1987-17.15621.641131.9297
32.98421.93171.66083.10271.86045.8909-0.21030.18790.265-0.00650.1794-0.1082-0.53750.41840.03090.1706-0.1013-0.0280.10170.01720.0752-18.352222.666-7.044
43.1089-0.05370.8995.6836-3.80326.44740.0678-0.0685-0.6412-0.0883-0.1143-0.46730.23350.76270.04640.07030.0219-0.00260.1844-0.08070.348-2.499420.231926.3707
50.38850.57180.34223.12291.02543.3345-0.03190.0638-0.0661-0.13350.0136-0.04520.10240.49140.01840.0644-0.0262-0.0120.12920.01990.0453-50.75769.706661.8769
63.58181.7838-4.78782.5396-3.48419.77480.0413-0.14330.07710.1289-0.0998-0.1395-0.2050.35750.05850.067-0.0328-0.01880.033-0.00540.114-47.63585.572126.575
73.03771.0539-0.03012.3966-0.72817.0486-0.1461-0.00420.3799-0.1888-0.03390.0139-0.4540.1780.17990.21-0.0622-0.0090.02210.00370.198-55.32330.416657.3955
81.0153-0.3311-0.39356.02231.59572.04190.00260.14810.0074-0.06910.04210.0109-0.13-0.0918-0.04470.09380.0062-0.00550.08270.02470.1221-61.812812.510825.0082
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 116
2X-RAY DIFFRACTION2H117 - 213
3X-RAY DIFFRACTION3L1 - 115
4X-RAY DIFFRACTION4L116 - 213
5X-RAY DIFFRACTION5C1 - 115
6X-RAY DIFFRACTION6C116 - 213
7X-RAY DIFFRACTION7B1 - 116
8X-RAY DIFFRACTION8B117 - 213

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