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- PDB-4m7z: Unliganded 1 crystal structure of S25-26 Fab -

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Basic information

Entry
Database: PDB / ID: 4m7z
TitleUnliganded 1 crystal structure of S25-26 Fab
Components(S25-26 Fab (Igg1k) ...) x 2
KeywordsIMMUNE SYSTEM / Beta-Sandwich / Carbohydrate/Sugar Binding
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsHaji-Ghassemi, O. / Evans, S.V. / Muller-Loennies, S. / Saldova, R. / Muniyappa, M. / Brade, L. / Rudd, P.M. / Harvey, D.J. / Kosma, P. / Brade, H.
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 12, 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 1.4Jul 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_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.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_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
B: S25-26 Fab (Igg1k) Heavy Chain
H: S25-26 Fab (Igg1k) Heavy Chain
C: S25-26 Fab (Igg1k) Light Chain
L: S25-26 Fab (Igg1k) Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,52823
Polymers95,7754
Non-polymers2,75319
Water2,234124
1
B: S25-26 Fab (Igg1k) Heavy Chain
C: S25-26 Fab (Igg1k) Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,54413
Polymers47,8882
Non-polymers1,65711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-27 kcal/mol
Surface area19620 Å2
MethodPISA
2
H: S25-26 Fab (Igg1k) Heavy Chain
L: S25-26 Fab (Igg1k) Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,98410
Polymers47,8882
Non-polymers1,0968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-26 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.298, 111.988, 156.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21H
12C
22L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010B4 - 217
2010H4 - 217
1020C1 - 217
2020L1 - 217

NCS ensembles :
ID
1
2

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Components

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Antibody , 2 types, 4 molecules BHCL

#1: Antibody S25-26 Fab (Igg1k) Heavy Chain


Mass: 23531.480 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) 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

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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 , 4 types, 141 molecules

#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.91 Å3/Da / Density % sol: 68.56 %
Crystal growTemperature: 289 K / pH: 7.5
Details: 0.2M calcium chloride, 0.1M HEPES, 28% (v/v) PEG 400 , pH 7.5, 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
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 27, 2012 / Details: VERTICAL FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.75→25 Å / Num. obs: 39918 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.3
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 7 % / Rmerge(I) obs: 0.672 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.75 Å29.44 Å
Translation2.75 Å29.44 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→24.76 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 22.987 / SU ML: 0.231 / SU R Cruickshank DPI: 0.5057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.506 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1997 5 %RANDOM
Rwork0.216 ---
obs0.217 39858 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.21 Å2
Baniso -1Baniso -2Baniso -3
1--3.39 Å20 Å20 Å2
2--6.97 Å20 Å2
3----3.59 Å2
Refinement stepCycle: LAST / Resolution: 2.75→24.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6672 0 177 124 6973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.027014
X-RAY DIFFRACTIONr_bond_other_d00.026492
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9639503
X-RAY DIFFRACTIONr_angle_other_deg3.6633.00215006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7995864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26623.978269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.861151084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6921528
X-RAY DIFFRACTIONr_chiral_restr0.0770.21058
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217758
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021562
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it023468
X-RAY DIFFRACTIONr_mcbond_other023467
X-RAY DIFFRACTIONr_mcangle_it034328
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B114820.11
12H114820.11
21C117260.13
22L117260.13
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 146 -
Rwork0.338 2766 -
obs--99.69 %
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)
13.0077-0.84722.98783.6599-0.63363.2593-0.0921-0.05340.17210.03820.08780.1415-0.1489-0.21730.00430.09460.02020.04580.1390.08890.129655.6762-10.0341-13.8901
25.2922-1.84261.14543.4802-1.11793.00480.06780.08910.19610.1685-0.02350.1825-0.1485-0.0523-0.04430.3379-0.03520.05610.14920.03320.126438.021915.5329-32.3935
37.0015-1.35560.88542.8375-1.29952.8389-0.0259-0.05330.57190.23260.00170.0885-0.503-0.0640.02420.3978-0.00340.05610.14920.02860.151835.843116.8478-31.3387
44.9872.78270.90123.3130.13323.6598-0.02640.43650.3491-0.1982-0.0335-0.2487-0.27290.22850.05990.12740.00450.04060.13740.09040.1426-8.5911-5.7895-6.6102
56.78231.953-0.10484.3125-1.17082.10050.2634-0.06770.96960.20270.31420.2822-0.4398-0.3626-0.57760.58490.12140.2860.56050.21130.61248.626223.919-18.1249
65.4388-0.54960.26233.8163-0.27634.06180.24470.27761.0176-0.34080.24150.1325-0.811-0.7052-0.48610.65960.12110.30940.44550.18260.67310.79923.4123-19.9828
74.9883-1.580.67133.6769-1.2791.8425-0.03850.20240.0896-0.0770.22760.2696-0.066-0.3014-0.18910.1499-0.03970.02030.1040.05530.053837.6543-20.7174-17.7696
811.04012.434313.53112.4977-5.266522.27580.30.6078-0.5130.26040.75710.55050.17190.3378-1.05710.20.01920.06580.56550.26050.316921.5234-8.1354-27.6945
93.87391.9055-2.60623.2392-3.6537.32710.049-0.0419-0.204-0.1155-0.024-0.00960.25110.1195-0.0250.21310.0575-0.02810.12150.08430.14735.12814.9997-42.8443
104.04581.0101-1.24933.3933-1.1633.5333-0.0015-0.02550.2531-0.16910.0109-0.3978-0.21310.404-0.00950.14560.0017-0.01870.1278-0.00860.11169.5741-8.4044.0923
1118.499215.62915.398733.60662.65061.78120.3511-0.63990.26080.6491-0.4193-0.8089-0.0044-0.20480.06820.41-0.15970.12570.44520.13310.537125.18767.4976-0.737
125.2171-2.93531.12497.6688-1.67723.6490.1364-0.52751.04041.0010.16490.075-1.25-0.6125-0.30130.90940.03170.36610.6509-0.08860.82511.690127.5254-3.8919
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B4 - 116
2X-RAY DIFFRACTION2B117 - 164
3X-RAY DIFFRACTION3B165 - 214
4X-RAY DIFFRACTION4H4 - 116
5X-RAY DIFFRACTION5H117 - 164
6X-RAY DIFFRACTION6H165 - 213
7X-RAY DIFFRACTION7C1 - 109
8X-RAY DIFFRACTION8C110 - 115
9X-RAY DIFFRACTION9C116 - 214
10X-RAY DIFFRACTION10L1 - 109
11X-RAY DIFFRACTION11L110 - 115
12X-RAY DIFFRACTION12L116 - 213

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