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- PDB-7rdl: Crystal structure of PCDN-22A, an anti-HIV antibody from the PCDN... -

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Basic information

Entry
Database: PDB / ID: 7rdl
TitleCrystal structure of PCDN-22A, an anti-HIV antibody from the PCDN bnAb lineage
Components
  • PCDN-22A Fab heavy chain
  • PCDN-22A Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / Immunoglobulin / Broadly Neutralizing
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsOmorodion, O. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
Bill & Melinda Gates FoundationOPP119635 United States
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structural and Biochemical Characterization of Cysteinylation in Broadly Neutralizing Antibodies to HIV-1.
Authors: Omorodion, O. / Wilson, I.A.
History
DepositionJul 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 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: PCDN-22A Fab light chain
B: PCDN-22A Fab heavy chain
C: PCDN-22A Fab light chain
D: PCDN-22A Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1506
Polymers96,9064
Non-polymers2442
Water1629
1
A: PCDN-22A Fab light chain
B: PCDN-22A Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5753
Polymers48,4532
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PCDN-22A Fab light chain
D: PCDN-22A Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5753
Polymers48,4532
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.079, 105.471, 145.926
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "C"
d_1ens_2(chain "B" and (resid 2 through 25 or resid 28 through 213))
d_2ens_2(chain "D" and (resid 2 through 126 or resid 135 through 205 or resid 208 through 213))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALGLUA1 - 215
d_21ens_1VALGLUC1 - 215
d_11ens_2VALTYRB1 - 24
d_12ens_2SERPROB27 - 217
d_21ens_2VALPROD1 - 138
d_22ens_2THRTHRD144 - 214
d_23ens_2ASPPROD217 - 222

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.992467371328, -0.0966249944392, -0.075313526667), (0.0703088954623, 0.0541980942836, -0.99605181883), (0.100325351075, -0.993844141214, -0.0469962435316)132.753543125, 92.0183196283, 75.7772745874
2given(-0.993592181847, -0.0991871240947, -0.054189395512), (0.0568935199669, -0.0246383929212, -0.998076187964), (0.0976611670928, -0.994763722704, 0.0301236192049)133.386449746, 98.2786806743, 72.4645559789

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Components

#1: Antibody PCDN-22A Fab light chain


Mass: 23538.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody PCDN-22A Fab heavy chain


Mass: 24914.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.37
Details: 0.1 M Tris, 0.2 M magnesium chloride, 8% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 29990 / % possible obs: 99.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 72.15 Å2 / CC1/2: 0.91 / Rpim(I) all: 0.07 / Rsym value: 0.15 / Net I/σ(I): 9
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1464 / CC1/2: 0.51 / Rpim(I) all: 0.7 / Rsym value: 1.59 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-20002.3.10data reduction
SCALEPACKdata scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BZD

5bzd


Resolution: 2.71→45.58 Å / SU ML: 0.417 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.3222
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2582 1502 5.02 %
Rwork0.2299 28417 -
obs0.2314 29919 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.99 Å2
Refinement stepCycle: LAST / Resolution: 2.71→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6645 0 16 9 6670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00226823
X-RAY DIFFRACTIONf_angle_d0.57849291
X-RAY DIFFRACTIONf_chiral_restr0.04271045
X-RAY DIFFRACTIONf_plane_restr0.00441181
X-RAY DIFFRACTIONf_dihedral_angle_d19.75032429
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.41824758265
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS1.43323045193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.790.41731480.39212448X-RAY DIFFRACTION96.4
2.79-2.890.47951250.36732551X-RAY DIFFRACTION99.37
2.89-3.010.35961360.34482568X-RAY DIFFRACTION99.48
3.01-3.150.34181340.30722528X-RAY DIFFRACTION99.14
3.15-3.310.32231320.2742595X-RAY DIFFRACTION99.74
3.31-3.520.32871660.24882569X-RAY DIFFRACTION99.6
3.52-3.790.2651310.25072552X-RAY DIFFRACTION98.97
3.79-4.170.26321360.20262605X-RAY DIFFRACTION99.78
4.17-4.770.21311280.16852613X-RAY DIFFRACTION99.56
4.78-6.010.18951330.19312654X-RAY DIFFRACTION99.15
6.01-45.580.2161330.22152734X-RAY DIFFRACTION97.95
Refinement TLS params.

Method: refined / 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)Origin x (Å)Origin y (Å)Origin z (Å)
14.50961840515-0.383095454520.3331526779733.29175560859-1.595944795855.88420042702-0.0773147406885-0.418756040236-0.4797631820140.06241600199010.0733554563719-0.04917054185370.7396616180431.017344093920.0307374261210.5597981638570.1534101579170.009868148730031.31651654975-0.09996394632520.46053821076356.458170780564.143874671859.2804192052
25.260833001141.38623652039-2.095509451683.9748482951-0.1983811565651.80841180366-0.3029600415970.04915888705110.678621693564-0.1962640996830.603764496198-0.152665965662-0.06389313137980.738268319328-0.3457134014770.6492930574380.197835709859-0.05583783595822.11204795691-0.2492783089740.58708388711782.819679953668.809410607240.1864515798
35.856481223584.71291080031-1.333153076869.60485176351-1.190433351932.4115519119-0.249470300294-0.1512400972910.09013557338890.2205263284380.52646102513-0.239456855612-0.4604475219020.709180977906-0.1736295738640.6776539696570.162849917939-0.03572309631822.02839920931-0.2219789076640.62112886817786.289539300669.548296038839.2682563873
41.95779438549-0.374269515176-0.7659967954653.20165780645-0.3613091525456.45179306463-0.01167981664910.2534813106910.226623583206-0.1724806586250.0350461455893-0.0830916418629-0.544950771612-0.1124289708940.05908604446770.5171748728580.0212883764031-0.08627661886361.25993301673-0.09903596246410.38192058438747.519948458979.489123977346.3717393946
52.95828627376-3.685031718360.7683587566948.25642985241-0.7246781175955.50782456611-0.5051687420060.34678170018-0.844787005747-0.2928279605381.099256023720.7522017313930.754475911650.353268141035-1.099556403250.681574010879-0.167347365349-0.1354476958222.31728684627-0.1510703544270.61695043626576.159229025365.341369165226.0759317288
62.25848240344-0.367434891367-0.7788174132121.22329644283-0.1350248722630.341448466635-0.322151494388-0.387060989898-1.067161669380.9985625338930.6898972541040.71781790476-0.793959522224-0.2418929666690.4581852029861.110790449240.4056534239550.1156194648211.454140664610.2786480011410.13846741869966.466536114340.073732366914.8239689548
72.9878267019-0.0764976327152-0.7233421921534.91392346226-1.954036765964.89759402115-0.6457279225220.277511673218-0.0749647095689-2.294989149750.3983621478331.018157520021.26299452288-0.414367963614-0.2180436725611.339504122680.0156162905908-0.3309855740461.250537010250.07199780433530.64962742335538.948881958562.39601024813.7323891511
86.85602975863-2.179735589970.3283263677416.81527665334-2.064791753048.225003184890.3706305633850.1817445725110.668013594537-0.451308815470.0272416699594-0.362844141703-0.9657559778170.277699108127-0.4648038606671.30484805088-0.09417244788120.1413426184181.098980401460.03010169885860.38024990114975.098500741854.2385608571-2.70974454451
91.34984282134-0.3621279891750.2197135352510.4614409235440.6913506759810.346794942060.66981898386-0.284050270682-0.161318275422-0.865910108224-0.198932215502-0.286843477021-0.607503935490.1790222338970.1481686510941.151795955680.07815069503630.1846865623541.231522917410.09946840670220.21596016419269.213732917755.02644693156.01961144193
101.0008395881-0.168635855826-1.510674764822.62547992154-0.8543015150996.845713408070.577715670244-0.9112394720480.0832575697927-1.24214678895-0.655632630007-0.487260094844-0.4835498122711.870470207010.1533507871791.3066007242-0.1187783176240.01602708067321.766850702560.03558332040750.51363458029250.493193468274.842937154215.8973768432
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 102 )AA-1 - 1021 - 104
22chain 'A' and (resid 103 through 163 )AA103 - 163105 - 165
33chain 'A' and (resid 164 through 213 )AA164 - 213166 - 215
44chain 'B' and (resid 2 through 119 )BB2 - 1191 - 133
55chain 'B' and (resid 120 through 213 )BB120 - 213134 - 217
66chain 'C' and (resid -1 through 102 )CC-1 - 1021 - 104
77chain 'C' and (resid 103 through 213 )CC103 - 213105 - 215
88chain 'D' and (resid 2 through 87 )DD2 - 871 - 87
99chain 'D' and (resid 88 through 134 )DD88 - 13488 - 143
1010chain 'D' and (resid 135 through 214 )DD135 - 214144 - 223

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