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- PDB-4yaq: Crystal structure of a computationally optimized PG9 mutant -

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Basic information

Entry
Database: PDB / ID: 4yaq
TitleCrystal structure of a computationally optimized PG9 mutant
Components
  • PG9_N100FY Fab heavy chain
  • PG9_N100FY Light Chain
KeywordsIMMUNE SYSTEM / Antibody / HIV
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / : / IGL@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMurrell, S. / Julien, J.P. / Wilson, I.A.
CitationJournal: J.Clin.Invest. / Year: 2015
Title: Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth.
Authors: Willis, J.R. / Sapparapu, G. / Murrell, S. / Julien, J.P. / Singh, V. / King, H.G. / Xia, Y. / Pickens, J.A. / LaBranche, C.C. / Slaughter, J.C. / Montefiori, D.C. / Wilson, I.A. / Meiler, J. / Crowe, J.E.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: PG9_N100FY Fab heavy chain
L: PG9_N100FY Light Chain
A: PG9_N100FY Fab heavy chain
B: PG9_N100FY Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,24312
Polymers100,1314
Non-polymers2,1128
Water3,045169
1
H: PG9_N100FY Fab heavy chain
L: PG9_N100FY Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4128
Polymers50,0652
Non-polymers1,3466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-24 kcal/mol
Surface area21590 Å2
MethodPISA
2
A: PG9_N100FY Fab heavy chain
B: PG9_N100FY Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8314
Polymers50,0652
Non-polymers7662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-2 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.740, 122.980, 69.920
Angle α, β, γ (deg.)90.00, 96.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules HALB

#1: Antibody PG9_N100FY Fab heavy chain


Mass: 27242.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): FreeStyle 293-F / Production host: Homo sapiens (human) / References: UniProt: A0A087X1C7
#2: Antibody PG9_N100FY Light Chain


Mass: 22823.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGL@ / Production host: Homo sapiens (human) / References: UniProt: Q6GMW3

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Sugars , 1 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 175 molecules

#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 5% PEG 3000, 40% PEG 400 and 0.1M MES

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 42379 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.9 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fab portion of 3U4E

3u4e


Resolution: 2.3→37.26 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 2000 4.72 %Random selection
Rwork0.2044 ---
obs0.206 42353 98.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→37.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6860 0 134 169 7163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027182
X-RAY DIFFRACTIONf_angle_d0.6979780
X-RAY DIFFRACTIONf_dihedral_angle_d12.0992572
X-RAY DIFFRACTIONf_chiral_restr0.0221086
X-RAY DIFFRACTIONf_plane_restr0.0031232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.37361430.31652893X-RAY DIFFRACTION99
2.3575-2.42120.32171450.30742903X-RAY DIFFRACTION99
2.4212-2.49250.33011410.28852870X-RAY DIFFRACTION98
2.4925-2.57290.31121410.27762848X-RAY DIFFRACTION98
2.5729-2.66480.29991440.25862891X-RAY DIFFRACTION99
2.6648-2.77150.28191440.25052900X-RAY DIFFRACTION99
2.7715-2.89760.30761430.24352887X-RAY DIFFRACTION99
2.8976-3.05030.28691420.24712869X-RAY DIFFRACTION98
3.0503-3.24130.29551410.23852850X-RAY DIFFRACTION98
3.2413-3.49140.2571440.21172905X-RAY DIFFRACTION99
3.4914-3.84240.24681430.19642879X-RAY DIFFRACTION98
3.8424-4.39770.18631410.16722853X-RAY DIFFRACTION97
4.3977-5.53770.1771420.15052871X-RAY DIFFRACTION98
5.5377-37.2650.18341460.16932934X-RAY DIFFRACTION98

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