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- PDB-5cip: Crystal Structure of Unbound 4E10 -

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Basic information

Entry
Database: PDB / ID: 5cip
TitleCrystal Structure of Unbound 4E10
Components
  • (FAB 4E10 HEAVY CHAIN) x 2
  • FAB 4E10 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / BROADLY NEUTRALIZING ANTIBODY / RECOMBINANT FAB / ENV-PEPTIDE / HIV-1 / EPITOPE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsCaaveiro, J.M.M. / Rujas, E. / Nieva, J.L. / Tsumoto, K.
Funding support United States, Japan, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI097051-01 United States
Japan Society for the Promotion of Science25249115 Japan
CitationJournal: J.Virol. / Year: 2015
Title: Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10
Authors: Rujas, E. / Gulzar, N. / Morante, K. / Tsumoto, K. / Scott, J.K. / Nieva, J.L. / Caaveiro, J.M.M.
History
DepositionJul 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 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

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Assembly

Deposited unit
H: FAB 4E10 HEAVY CHAIN
L: FAB 4E10 LIGHT CHAIN
A: FAB 4E10 HEAVY CHAIN
B: FAB 4E10 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)93,8084
Polymers93,8084
Non-polymers00
Water2,414134
1
H: FAB 4E10 HEAVY CHAIN
L: FAB 4E10 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)46,9682
Polymers46,9682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-24 kcal/mol
Surface area20160 Å2
MethodPISA
2
A: FAB 4E10 HEAVY CHAIN
B: FAB 4E10 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)46,8392
Polymers46,8392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-23 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.660, 134.170, 81.860
Angle α, β, γ (deg.)90.00, 105.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody FAB 4E10 HEAVY CHAIN


Mass: 23861.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T7 Shuffle
#2: Antibody FAB 4E10 LIGHT CHAIN


Mass: 23106.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T7 Shuffle
#3: Antibody FAB 4E10 HEAVY CHAIN


Mass: 23732.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T7 Shuffle
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCES OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...THE SEQUENCES OF THIS PROTEIN WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.68 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100mM MES, 15% PEG 20,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.688
11H, -K, -H-L20.312
ReflectionResolution: 2.48→44.7 Å / Num. obs: 32268 / % possible obs: 98.4 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.7
Reflection shellResolution: 2.48→2.61 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 4.2 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WY7

4wy7


Resolution: 2.48→42.97 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.886 / SU B: 7.434 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SF FILE CONTAINS. FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23119 1632 5.1 %RANDOM
Rwork0.18302 ---
obs0.1854 30609 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.276 Å2
Baniso -1Baniso -2Baniso -3
1--10.37 Å20 Å2-6.28 Å2
2--30.76 Å20 Å2
3----20.39 Å2
Refinement stepCycle: 1 / Resolution: 2.48→42.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6527 0 0 134 6661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.026704
X-RAY DIFFRACTIONr_bond_other_d0.0010.026219
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9519132
X-RAY DIFFRACTIONr_angle_other_deg0.7053.00114360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2255.023867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19223.696257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.215151050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6511536
X-RAY DIFFRACTIONr_chiral_restr0.0680.21034
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021514
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_it1.5082.5043460
X-RAY DIFFRACTIONr_mcbond_other1.5082.5043459
X-RAY DIFFRACTIONr_mcangle_it2.7263.7494316
X-RAY DIFFRACTIONr_mcangle_other2.7263.7494317
X-RAY DIFFRACTIONr_scbond_it1.1222.6153244
X-RAY DIFFRACTIONr_scbond_other1.1222.6153244
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9783.8734813
X-RAY DIFFRACTIONr_long_range_B_refined3.86220.0726900
X-RAY DIFFRACTIONr_long_range_B_other3.85520.0736891
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.479→2.543 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 118 -
Rwork0.225 2152 -
obs--96.23 %

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