[English] 日本語
Yorodumi
- PDB-7rdk: Crystal structure of PCDN-16B, an anti-HIV antibody from the PCDN... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
Non-polymers , 5 types, 80 molecules

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


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


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


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


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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more