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- PDB-7rdk: Crystal structure of PCDN-16B, an anti-HIV antibody from the PCDN... -

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Basic information

Entry
Database: PDB / ID: 7rdk
TitleCrystal structure of PCDN-16B, an anti-HIV antibody from the PCDN bnAb lineage (cysteinylated state)
Components(PCDN-16B Fab ...) x 2
KeywordsIMMUNE SYSTEM / Antibody / Broadly Neutralizing / HIV-1 / Cysteinylation
Function / homologyCYSTEINE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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 23, 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-16B Fab light chain
B: PCDN-16B Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7117
Polymers48,2782
Non-polymers4335
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-33 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.211, 115.230, 44.104
Angle α, β, γ (deg.)90.000, 99.085, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody PCDN-16B Fab light chain


Mass: 23458.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody PCDN-16B Fab heavy chain


Mass: 24818.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 80 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M lithium sulfate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. obs: 14022 / % possible obs: 94 % / Redundancy: 2.3 % / Biso Wilson estimate: 36.68 Å2 / CC1/2: 0.83 / Rpim(I) all: 0.09 / Rsym value: 0.12 / Net I/σ(I): 7.1
Reflection shellResolution: 2.46→2.54 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 659 / CC1/2: 0.48 / Rpim(I) all: 0.41 / Rsym value: 0.52 / % possible all: 92.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-20002.3.10data reduction
SCALEPACKdata scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BZD

5bzd


Resolution: 2.46→43.55 Å / SU ML: 0.4126 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.9039
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2533 702 5.01 %
Rwork0.2078 13301 -
obs0.2103 14003 92.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.64 Å2
Refinement stepCycle: LAST / Resolution: 2.46→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 26 75 3473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00193485
X-RAY DIFFRACTIONf_angle_d0.51564745
X-RAY DIFFRACTIONf_chiral_restr0.0407531
X-RAY DIFFRACTIONf_plane_restr0.0051608
X-RAY DIFFRACTIONf_dihedral_angle_d14.34251248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.650.35331010.31292415X-RAY DIFFRACTION83.26
2.65-2.910.38671290.29162668X-RAY DIFFRACTION92.89
2.91-3.330.29671450.2482719X-RAY DIFFRACTION94.4
3.33-4.20.2351720.18372754X-RAY DIFFRACTION96
4.2-43.550.19011550.15492745X-RAY DIFFRACTION94.03
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)
14.26888768054-0.004550458075480.2902504355276.035630859660.3364168035047.10483926268-0.0274900109408-0.0137620623422-0.214919462164-0.1798324683810.2285546953010.2880984890260.407169204797-0.189741378864-0.1651231983220.318669041084-0.05682853828110.0281968589970.197156269781-0.03536692165930.362396108281201.464-51.654102.269
20.475143464837-0.2200061232270.9137586266962.20232698762-2.21797639893.271887320140.26425089981-0.0708015759176-0.204662965602-0.2606096830920.214328810220.3319349808180.327797295457-0.00324347341076-0.480957063190.2408299811920.0408144089684-0.02120059469460.180844495674-0.06023505208810.370623824186199.467-48.74698.209
33.393500784382.843297242770.6526978725326.823053353880.162849081730.855901930462-0.04133818366010.1922135163430.34912410585-0.3015840655810.111159278814-0.1231620282110.0126984563955-0.0289372971772-0.0439453895510.2329164261520.04557557125040.06369965270510.26121262964-0.002817358290020.338358550245203.268-19.69784.337
40.716844559681-0.0170844285120.6067382423624.54511308599-0.8367634965612.471848382780.291254675729-0.1152699222420.5876655520180.6555704166510.393420019968-0.113935894149-0.3945234248430.167047763664-0.5687713954270.4418920283330.023400084540.1910620469320.280057016579-0.07673409675210.495506321037207.204-37.159119.909
54.90974167191-3.111140360782.65222331944.91860293508-0.8715236320796.09716888226-0.0757933797620.119475045494-0.3370906783540.4812496410810.38660483482-0.6414113890180.1781767076120.933963438361-0.3558461834540.3153033271440.00827205113050.04511256518490.252779246671-0.1581115934240.61070584779214.741-43.641114.988
62.765380735112.038450562552.479016193917.35767229444-2.009873042574.92148708078-0.113101206412-0.236991909734-0.2911885047470.917880330677-0.206891322439-0.5733636995930.1757072712820.6093454523090.2371734292950.3789051316070.0547633185534-0.1019007279810.305978306504-0.0893291224270.308867367062214.387-38.465123.342
72.03082990969-2.503713251840.689292925019.28011396989-3.426512613591.59672869432-0.0773664996331-0.0553649869207-0.308177911391-0.2463115558840.3316552719540.3728191590030.03706045323560.0759567392371-0.1649200938190.302711113239-0.0009920128762830.1046296943150.308631733492-0.1135115533280.442671582675210.943-48.285118.085
80.9087938632-0.4709975353190.489779348852.46449554851-1.055591136230.6099280142180.01642155441170.0968475266204-0.0113983383416-0.05877490277420.018737986320.0418635600039-0.0372350646910.0228842979697-0.01408155512770.2678688897830.06714242665310.1117224218920.290928185878-0.1571512344490.395332247666201.697-25.62102.365
95.25664966199-0.4766420015890.8786373879750.99939360496-1.251159818461.56564723171-0.265003886202-1.13646130510.271118346570.3239389163630.1830505209370.00571837414898-0.219873697385-0.572604464114-0.1508799816720.2711464451170.05574300942430.06462915512420.448741957557-0.02693863454760.252522428899197.289-16.12798.97
105.06072379322-1.81429136091.415340341146.5934737592-0.292874398980.403933643319-0.223675022945-0.6105300614090.02385234934390.1650570786940.02950508484551.36688542241-0.0770977295935-0.6828412109560.05611964329920.113260835552-0.08322441029350.01038635535890.533576169569-0.02349929354640.351428913697185.839-19.17796.02
115.080729322830.8105692375992.45717899972.987568950110.2923831226913.243377363840.181589499789-0.408827684757-0.08356602426550.141189348871-0.00277481977299-0.157930570283-0.25774622035-0.359459669418-0.177001708170.225604760419-0.02122259152050.1394980270560.288083299426-0.0489729872280.364219849737195.25-16.03195.572
123.48356030299-0.7278260331194.167893768833.96782707876-0.3575860750585.16958737155-0.620150828579-0.2621441576671.213919598430.08702860157720.227949423662-0.732704888161-0.5600880834990.5015302996530.2565464320420.3714150151430.1159205682890.04819222751510.624838916767-0.2131949014370.818794123172194.105-8.05698.073
135.052724722087.91715455918.558908021761.999975510772.000042785672.000001215180.302120469165-1.10184826034-0.0001756083177710.5129428777420.2651543042141.14610282567-0.2031012761650.964871801237-0.4934533765550.3367154404420.1878363031740.1856146076690.6754156186330.01063735239540.643480003872202.751-52.78117.248
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-IDBeg PDB ins codeEnd PDB ins code
11( CHAIN A AND RESID 0:61 )A0 - 61
22( CHAIN A AND RESID 62:113 )A62 - 113
33( CHAIN A AND RESID 114:214 )A114 - 214
44( CHAIN B AND RESID 1:40 )B1 - 40
55( CHAIN B AND RESID 41:63 )B41 - 63
66( CHAIN B AND RESID 64:82 )B64 - 82
77( CHAIN B AND RESID 82:102 )B82 - 102AG
88( CHAIN B AND RESID 100:134 )B100 - 134H
99( CHAIN B AND RESID 135:154 )B135 - 154
1010( CHAIN B AND RESID 155:165 )B155 - 165
1111( CHAIN B AND RESID 166:200 )B166 - 200
1212( CHAIN B AND RESID 201:216 )B201 - 216
1313( CHAIN B AND RESID 301:301 )B301

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