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- PDB-6be2: Crystal structure of a polysaccharide-binding human Fab (F598) -

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Basic information

Entry
Database: PDB / ID: 6be2
TitleCrystal structure of a polysaccharide-binding human Fab (F598)
Components
  • Fab (F598) Heavy Chain
  • Fab (F598) Light Chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / human antibody / antigen binding fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,2982
Polymers47,2982
Non-polymers00
Water9,710539
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-19 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.837, 104.067, 104.300
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-386-

HOH

21L-426-

HOH

31L-552-

HOH

41L-556-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 4000, 20% iso-propanol, 0.1 M sodium citrate pH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.69→30.914 Å / Num. obs: 54253 / % possible obs: 99.7 % / Redundancy: 7.3 % / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.055 / Net I/σ(I): 25.19
Reflection shellResolution: 1.69→1.79 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 3.08 / Num. unique obs: 8588 / CC1/2: 0.877 / Rrim(I) all: 0.877 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LLD, 5EOR, 3MLX

4lld

5eor

3mlx


Resolution: 1.7→30.914 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.6
RfactorNum. reflection% reflection
Rfree0.2099 2000 3.75 %
Rwork0.171 --
obs0.1724 53356 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→30.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 0 539 3770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053334
X-RAY DIFFRACTIONf_angle_d0.8814561
X-RAY DIFFRACTIONf_dihedral_angle_d14.9851991
X-RAY DIFFRACTIONf_chiral_restr0.056
X-RAY DIFFRACTIONf_plane_restr0.006582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74250.29251420.24313651X-RAY DIFFRACTION100
1.7425-1.78960.26711410.23073617X-RAY DIFFRACTION100
1.7896-1.84230.27981410.23023638X-RAY DIFFRACTION100
1.8423-1.90170.28171420.21893638X-RAY DIFFRACTION100
1.9017-1.96970.22061400.19683604X-RAY DIFFRACTION100
1.9697-2.04860.23841430.18883662X-RAY DIFFRACTION100
2.0486-2.14180.21941410.18313637X-RAY DIFFRACTION100
2.1418-2.25470.23941420.18083626X-RAY DIFFRACTION100
2.2547-2.39590.19871440.18843680X-RAY DIFFRACTION100
2.3959-2.58080.22661410.18343646X-RAY DIFFRACTION100
2.5808-2.84030.21751440.17973705X-RAY DIFFRACTION100
2.8403-3.25090.19241440.17483695X-RAY DIFFRACTION100
3.2509-4.09430.20061450.14543709X-RAY DIFFRACTION100
4.0943-30.9140.17291500.13773848X-RAY DIFFRACTION100
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)
14.68670.4088-0.10731.71620.1661.31180.03170.22110.3736-0.05450.00030.1691-0.1697-0.0626-0.0270.17920.00350.01960.11690.02330.156113.584929.5403-3.5867
20.8675-0.1804-0.38111.91350.66734.3210.22790.1359-0.0074-0.30580.12680.1147-0.1621-0.6288-0.21050.21120.03260.01640.29440.07370.189425.40115.4459-26.3708
34.88810.08293.07973.3595-0.52528.13410.16180.05390.0858-0.23750.33170.4775-0.4288-0.5054-0.26040.22660.06050.04170.26790.09850.246225.014915.443-30.8968
41.7440.5432-0.05573.74531.02741.6895-0.02090.1479-0.0855-0.06980.06440.0061-0.0356-0.0571-0.04050.1213-0.0040.00230.1358-0.03270.16081.599311.6462-2.6906
56.76051.3043-2.91151.15760.36422.9393-0.25190.3834-0.7147-0.05840.0584-0.12560.3228-0.30680.16480.2311-0.03270.01830.2334-0.01560.239827.9232-1.0435-27.8696
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 178 )
3X-RAY DIFFRACTION3chain 'H' and (resid 179 through 224 )
4X-RAY DIFFRACTION4chain 'L' and (resid 1 through 111 )
5X-RAY DIFFRACTION5chain 'L' and (resid 112 through 213 )

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