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- PDB-6ltg: Crystal structure of the Fab fragment of murine monoclonal antibo... -

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Basic information

Entry
Database: PDB / ID: 6ltg
TitleCrystal structure of the Fab fragment of murine monoclonal antibody OHV-3 against Human herpesvirus 6B
Components
  • antibody Fab fragment H-chain
  • antibody Fab fragment L-chain
KeywordsIMMUNE SYSTEM / Human herpesvirus 6B / neutralizing antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsNishimura, M. / Novita, B.D. / Kato, T. / Tjan, L.H. / Wang, B. / Wakata, A. / Poetranto, A.L. / Kawabata, A. / Tang, H. / Aoshi, T. / Mori, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP17im0210601 Japan
Japan Society for the Promotion of Science (JSPS)JP19K06512 Japan
CitationJournal: Plos Pathog. / Year: 2020
Title: Structural basis for the interaction of human herpesvirus 6B tetrameric glycoprotein complex with the cellular receptor, human CD134.
Authors: Nishimura, M. / Novita, B.D. / Kato, T. / Handayani Tjan, L. / Wang, B. / Wakata, A. / Lystia Poetranto, A. / Kawabata, A. / Tang, H. / Aoshi, T. / Mori, Y.
History
DepositionJan 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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
Revision 1.2Nov 29, 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 1.3Oct 9, 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

Downloads & links

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Assembly

Deposited unit
A: antibody Fab fragment H-chain
B: antibody Fab fragment L-chain
C: antibody Fab fragment H-chain
D: antibody Fab fragment L-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9726
Polymers94,9244
Non-polymers492
Water23,9961332
1
A: antibody Fab fragment H-chain
B: antibody Fab fragment L-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4863
Polymers47,4622
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-30 kcal/mol
Surface area19420 Å2
MethodPISA
2
C: antibody Fab fragment H-chain
D: antibody Fab fragment L-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4863
Polymers47,4622
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-31 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.380, 95.200, 113.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein antibody Fab fragment H-chain


Mass: 23677.713 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody antibody Fab fragment L-chain


Mass: 23784.127 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1332 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM BIS-Tris pH 6.5, 0.2 M MgCl2, polyethylene glycol 3350 23% (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→38.645 Å / Num. obs: 212352 / % possible obs: 99.6 % / Redundancy: 3.561 % / Biso Wilson estimate: 26.579 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.07 / Χ2: 1.015 / Net I/σ(I): 13.4 / Num. measured all: 756090 / Scaling rejects: 197
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.63-1.673.6460.711.855732615756157240.6550.83599.8
1.67-1.723.6430.612.175582415349153220.7350.71799.8
1.72-1.773.6380.4732.825438514986149500.8120.55699.8
1.77-1.823.6280.3633.665253614505144800.8750.42799.8
1.82-1.883.6230.2874.615099314093140730.9210.33799.9
1.88-1.953.6030.2126.194892513604135780.9550.24999.8
1.95-2.023.5770.1667.734687613134131040.9710.19699.8
2.02-2.13.5380.1349.514449512608125770.980.15999.8
2.1-2.23.4720.10811.274213912173121370.9880.12899.7
2.2-2.313.3340.08813.093820211524114590.9910.10599.4
2.31-2.433.1670.07714.343464611027109410.9920.09399.2
2.43-2.583.5540.06717.333691610438103860.9950.07899.5
2.58-2.763.3460.05320.5932263975696410.9960.06398.8
2.76-2.983.4690.04325.1931619916491150.9970.0599.5
2.98-3.263.7790.03630.2331541835883470.9980.04299.9
3.26-3.643.7610.0335.5228378756075460.9980.03599.8
3.64-4.213.7140.02938.0124759669566660.9980.03499.6
4.21-5.153.6990.02641.4620776563956170.9980.0399.6
5.15-7.293.6390.02638.3815864437343600.9990.03199.7
7.29-38.6453.2750.02239.457627237523290.9990.02798.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WCY

4wcy


Resolution: 1.63→38.645 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.3 / Phase error: 19.57
RfactorNum. reflection% reflection
Rfree0.2036 3855 1.82 %
Rwork0.182 --
obs0.1824 212335 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 60.66 Å2 / Biso mean: 23.8584 Å2 / Biso min: 4.13 Å2
Refinement stepCycle: final / Resolution: 1.63→38.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6586 0 2 1332 7920
Biso mean--12.31 33.85 -
Num. residues----864
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.63-1.64990.3321360.29367395100
1.6499-1.67080.31231390.26627535100
1.6708-1.69280.2481350.25977443100
1.6928-1.71590.30661350.25547419100
1.7159-1.74050.25011360.23167490100
1.7405-1.76640.25541390.22477492100
1.7664-1.7940.21571380.2137396100
1.794-1.82340.25041350.21477472100
1.8234-1.85490.24351410.20927487100
1.8549-1.88860.21751400.19747428100
1.8886-1.92490.20261360.19057515100
1.9249-1.96420.24391400.17887426100
1.9642-2.00690.18741400.17697425100
2.0069-2.05360.21451380.1717525100
2.0536-2.1050.18961330.17747381100
2.105-2.16190.1921420.17877497100
2.1619-2.22550.2281330.1837454100
2.2255-2.29730.24681350.1837739499
2.2973-2.37940.20651380.1872744799
2.3794-2.47470.23691370.1907741999
2.4747-2.58730.18491390.1877424100
2.5873-2.72360.22021390.1843742299
2.7236-2.89420.23141380.1836737899
2.8942-3.11760.17291400.17757457100
3.1176-3.43120.18031410.16197442100
3.4312-3.92730.16691360.15527490100
3.9273-4.94630.13361380.14877417100
4.9463-38.6450.23891380.1918741099

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