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- PDB-3muh: Crystal structure of PG9 light chain -

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Basic information

Entry
Database: PDB / ID: 3muh
TitleCrystal structure of PG9 light chain
ComponentsAntibody PG9 light chain
KeywordsIMMUNE SYSTEM / PG9 / HIV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPejchal, R. / Walker, L.M. / Burton, D.R. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structure and function of broadly reactive antibody PG16 reveal an H3 subdomain that mediates potent neutralization of HIV-1.
Authors: Pejchal, R. / Walker, L.M. / Stanfield, R.L. / Phogat, S.K. / Koff, W.C. / Poignard, P. / Burton, D.R. / Wilson, I.A.
History
DepositionMay 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_label_seq_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 2.1Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.2Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Antibody PG9 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2482
Polymers22,8231
Non-polymers4241
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.430, 87.430, 198.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Antibody Antibody PG9 light chain


Mass: 22823.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293S GnTI -/- / Production host: Homo sapiens (human)
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.8 Å3/Da / Density % sol: 74.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 40% ethanol, 0.05M magnesium chloride, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 13, 2009 / Details: mirrors
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. all: 9778 / Num. obs: 9135 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Biso Wilson estimate: 99.14 Å2 / Rsym value: 0.094 / Net I/σ(I): 21.8
Reflection shellResolution: 2.99→3.06 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 3.68 / Num. unique all: 672 / Rsym value: 0.69 / % possible all: 96.6

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LGV

1lgv


Resolution: 3→28 Å / Cor.coef. Fo:Fc: 0.9001 / Cor.coef. Fo:Fc free: 0.8764 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 732 8.15 %RANDOM
Rwork0.2454 ---
obs0.248 8978 93.4 %-
all-8978 --
Displacement parametersBiso mean: 81.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.6204 Å20 Å20 Å2
2--0.6204 Å20 Å2
3----1.2408 Å2
Refine analyzeLuzzati coordinate error obs: 0.75 Å
Refinement stepCycle: LAST / Resolution: 3→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1563 0 28 2 1593
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0116302
X-RAY DIFFRACTIONt_angle_deg1.3422272
X-RAY DIFFRACTIONt_dihedral_angle_d5202
X-RAY DIFFRACTIONt_trig_c_planes332
X-RAY DIFFRACTIONt_gen_planes2415
X-RAY DIFFRACTIONt_it163020
X-RAY DIFFRACTIONt_omega_torsion3.15
X-RAY DIFFRACTIONt_other_torsion21.77
X-RAY DIFFRACTIONt_chiral_improper_torsion2305
X-RAY DIFFRACTIONt_ideal_dist_contact17104
Refinement TLS params.

Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å / 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)
10.1784-0.00070.7627-0.0001-0.04862.77740.0191-0.0819-0.01870.0842-0.00330.0677-0.0240.0102-0.01570.0141-0.0091-0.04770.005-0.0271-0.1321
20.19010.13720.54140.12210.27281.5126-0.0076-0.0175-0.01270.02420.04710.093-0.0231-0.0178-0.0395-0.0044-0.0066-0.0805-0.0071-0.0645-0.1464
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L2 - 112
2X-RAY DIFFRACTION1L502 - 503
3X-RAY DIFFRACTION2L113 - 213

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