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- PDB-6be3: Crystal structure of a polysaccharide-binding human Fab (F598) in... -

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Basic information

Entry
Database: PDB / ID: 6be3
TitleCrystal structure of a polysaccharide-binding human Fab (F598) in complex with N-acetyl-D-glucosamine (GlcNAc)
Components
  • Fab (F598) Heavy Chain
  • Fab (F598) Light Chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / human antibody / antigen binding fragment / N-acetyl-D-glucosamine / complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSoliman, C. / Ramsland, P.A.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for antibody targeting of the broadly expressed microbial polysaccharide poly-N-acetylglucosamine.
Authors: Soliman, C. / Walduck, A.K. / Yuriev, E. / Richards, J.S. / Cywes-Bentley, C. / Pier, G.B. / Ramsland, P.A.
History
DepositionOct 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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 / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 4, 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

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Assembly

Deposited unit
H: Fab (F598) Heavy Chain
L: Fab (F598) Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5193
Polymers47,2982
Non-polymers2211
Water11,836657
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-12 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.263, 103.772, 105.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11L-416-

HOH

21L-438-

HOH

31L-611-

HOH

41L-618-

HOH

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Components

#1: Antibody Fab (F598) Heavy Chain


Mass: 24176.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab (F598) Light Chain


Mass: 23120.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#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.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / 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: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 4000, 20% iso-propanol, 0.1 M sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→32.254 Å / Num. obs: 64007 / % possible obs: 98.6 % / Redundancy: 7.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.099 / Net I/σ(I): 13.16
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.382 / Num. unique obs: 10070 / CC1/2: 0.949 / Rrim(I) all: 0.412 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BE2

6be2


Resolution: 1.6→32.254 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.42
RfactorNum. reflection% reflection
Rfree0.1998 2000 3.13 %
Rwork0.1663 --
obs0.1673 63942 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→32.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 15 657 3903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063332
X-RAY DIFFRACTIONf_angle_d0.8644556
X-RAY DIFFRACTIONf_dihedral_angle_d13.3061983
X-RAY DIFFRACTIONf_chiral_restr0.056518
X-RAY DIFFRACTIONf_plane_restr0.006579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64010.1971400.19094359X-RAY DIFFRACTION99
1.6401-1.68440.21271430.18014419X-RAY DIFFRACTION100
1.6844-1.7340.21861430.17744406X-RAY DIFFRACTION100
1.734-1.78990.19861440.1814462X-RAY DIFFRACTION100
1.7899-1.85390.19981430.18444430X-RAY DIFFRACTION100
1.8539-1.92810.23151420.19064418X-RAY DIFFRACTION100
1.9281-2.01580.22321440.17984430X-RAY DIFFRACTION100
2.0158-2.12210.17281430.17334449X-RAY DIFFRACTION100
2.1221-2.2550.1991440.17584447X-RAY DIFFRACTION100
2.255-2.42910.19961440.18024467X-RAY DIFFRACTION100
2.4291-2.67340.21531440.17464463X-RAY DIFFRACTION100
2.6734-3.060.20191450.16784505X-RAY DIFFRACTION100
3.06-3.85430.20331470.14614510X-RAY DIFFRACTION100
3.8543-32.26020.18121340.14864177X-RAY DIFFRACTION89
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)
13.22190.334-0.27420.82390.2481.23320.00490.22050.2396-0.04180.01550.0707-0.1213-0.028-0.02230.12040.00150.00210.08180.01960.123513.825429.5663-3.3191
21.49360.09980.9961.60941.62895.22550.10230.1086-0.0013-0.30550.0972-0.0048-0.196-0.0803-0.14090.16440.0028-0.00420.17250.01350.122427.736616.5212-26.1289
34.2360.46122.40893.21560.04156.92270.06170.07550.0209-0.16720.12250.271-0.0282-0.1987-0.14970.14290.03510.01550.17940.02910.160423.648715.1486-30.4588
41.55910.1938-0.09943.51561.28791.7171-0.01170.1117-0.1349-0.10430.0435-0.0070.0266-0.1164-0.02540.0892-0.0105-0.00090.0967-0.0140.11141.850911.6421-2.7807
55.67920.6043-2.36781.33690.26922.6126-0.17060.1699-0.4679-0.05640.0669-0.15820.2358-0.19280.09080.1984-0.01960.0110.1619-0.01170.183328.0745-0.9277-28.1485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 120 )
2X-RAY DIFFRACTION2chain 'H' and (resid 121 through 168 )
3X-RAY DIFFRACTION3chain 'H' and (resid 169 through 224 )
4X-RAY DIFFRACTION4chain 'L' and (resid 1 through 111 )
5X-RAY DIFFRACTION5chain 'L' and (resid 112 through 213 )

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