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- PDB-7t86: Crystal Structure of Fab CR5133 / Phospho-SD Peptide Complex -

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Basic information

Entry
Database: PDB / ID: 7t86
TitleCrystal Structure of Fab CR5133 / Phospho-SD Peptide Complex
Components
  • Antibody Fab CR5133 Heavy Chain
  • Antibody Fab CR5133 Light Chain
  • Phospho-SD Peptide
KeywordsTOXIN / Staphylcoccus aureus / SD Repeat / Phospho SD peptide / Fab / CR5133
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
Model detailsCrystal Structure of Fab CR5133 / Phospho-SD Peptide Complex
AuthorsLuo, J. / Malia, T.J. / Buckley, P.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Host Microbe / Year: 2023
Title: Multivalent human antibody-centyrin fusion protein to prevent and treat Staphylococcus aureus infections.
Authors: Buckley, P.T. / Chan, R. / Fernandez, J. / Luo, J. / Lacey, K.A. / DuMont, A.L. / O'Malley, A. / Brezski, R.J. / Zheng, S. / Malia, T. / Whitaker, B. / Zwolak, A. / Payne, A. / Clark, D. / ...Authors: Buckley, P.T. / Chan, R. / Fernandez, J. / Luo, J. / Lacey, K.A. / DuMont, A.L. / O'Malley, A. / Brezski, R.J. / Zheng, S. / Malia, T. / Whitaker, B. / Zwolak, A. / Payne, A. / Clark, D. / Sigg, M. / Lacy, E.R. / Kornilova, A. / Kwok, D. / McCarthy, S. / Wu, B. / Morrow, B. / Nemeth-Seay, J. / Petley, T. / Wu, S. / Strohl, W.R. / Lynch, A.S. / Torres, V.J.
History
DepositionDec 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 24, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Antibody Fab CR5133 Light Chain
H: Antibody Fab CR5133 Heavy Chain
A: Antibody Fab CR5133 Light Chain
B: Antibody Fab CR5133 Heavy Chain
C: Antibody Fab CR5133 Light Chain
D: Antibody Fab CR5133 Heavy Chain
E: Antibody Fab CR5133 Light Chain
F: Antibody Fab CR5133 Heavy Chain
G: Phospho-SD Peptide
I: Phospho-SD Peptide
J: Phospho-SD Peptide
K: Phospho-SD Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,66116
Polymers195,77712
Non-polymers8854
Water20,2491124
1
L: Antibody Fab CR5133 Light Chain
H: Antibody Fab CR5133 Heavy Chain
I: Phospho-SD Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1654
Polymers48,9443
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Antibody Fab CR5133 Light Chain
B: Antibody Fab CR5133 Heavy Chain
J: Phospho-SD Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1654
Polymers48,9443
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Antibody Fab CR5133 Light Chain
D: Antibody Fab CR5133 Heavy Chain
G: Phospho-SD Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1654
Polymers48,9443
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Antibody Fab CR5133 Light Chain
F: Antibody Fab CR5133 Heavy Chain
K: Phospho-SD Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1654
Polymers48,9443
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.981, 82.862, 90.652
Angle α, β, γ (deg.)70.890, 84.410, 62.100
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Antibody
Antibody Fab CR5133 Light Chain


Mass: 23096.602 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Antibody
Antibody Fab CR5133 Heavy Chain


Mass: 24616.535 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein/peptide
Phospho-SD Peptide


Mass: 1231.009 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: 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.: 4 / Source method: obtained synthetically / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.62 Å3/Da / Density % sol: 53.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M MES, 12.9% PEG 10000, 5%dioxane, 0.1 M beta-NADH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2017 / Details: mirrors
RadiationMonochromator: ACCEL SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.898→85.463 Å / Num. obs: 150662 / % possible obs: 95.9 % / Redundancy: 1.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.033 / Rrim(I) all: 0.047 / Net I/σ(I): 7.4 / Num. measured all: 274016
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.8 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.898-1.9050.325267214590.8240.3250.462.191
8.808-85.4630.049281815580.8910.0490.06911.998.3

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Processing

Software
NameVersionClassification
PHENIX1.8-3855refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4tw1

4tw1


Resolution: 1.9→68.32 Å / SU ML: 0.2284 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.0744
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2221 1988 1.32 %
Rwork0.1958 148623 -
obs0.1962 150611 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.75 Å2
Refinement stepCycle: LAST / Resolution: 1.9→68.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13121 0 56 1124 14301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006213494
X-RAY DIFFRACTIONf_angle_d0.870718351
X-RAY DIFFRACTIONf_chiral_restr0.05542056
X-RAY DIFFRACTIONf_plane_restr0.00592348
X-RAY DIFFRACTIONf_dihedral_angle_d18.71764819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.34131360.308610438X-RAY DIFFRACTION94.52
1.95-20.34071380.282410542X-RAY DIFFRACTION94.96
2-2.060.27961550.271310549X-RAY DIFFRACTION95.38
2.06-2.120.31471370.259810595X-RAY DIFFRACTION95.57
2.12-2.20.29111470.251710538X-RAY DIFFRACTION95.34
2.2-2.290.27391260.241810650X-RAY DIFFRACTION95.84
2.29-2.390.24921410.235910629X-RAY DIFFRACTION95.99
2.39-2.520.24431430.23210673X-RAY DIFFRACTION96.25
2.52-2.680.26791450.227410624X-RAY DIFFRACTION96.09
2.68-2.880.28481460.222810604X-RAY DIFFRACTION95.95
2.88-3.170.21471400.207810616X-RAY DIFFRACTION95.91
3.17-3.630.23271440.183510664X-RAY DIFFRACTION96.29
3.63-4.570.16861400.155110730X-RAY DIFFRACTION96.66
4.57-68.320.17131500.154210771X-RAY DIFFRACTION97.51

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