[English] 日本語
Yorodumi
- PDB-6rco: PfRH5-binding monoclonal antibody R5.004 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rco
TitlePfRH5-binding monoclonal antibody R5.004
Components
  • R5.004 heavy chain
  • R5.004 light chain
KeywordsIMMUNE SYSTEM / Plasmodium falciparum Erythrocyte invasion Neutralisation Human monoclonal antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsAlanine, D.G.W. / Draper, S.J. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Cell / Year: 2019
Title: Human Antibodies that Slow Erythrocyte Invasion Potentiate Malaria-Neutralizing Antibodies.
Authors: Alanine, D.G.W. / Quinkert, D. / Kumarasingha, R. / Mehmood, S. / Donnellan, F.R. / Minkah, N.K. / Dadonaite, B. / Diouf, A. / Galaway, F. / Silk, S.E. / Jamwal, A. / Marshall, J.M. / Miura, ...Authors: Alanine, D.G.W. / Quinkert, D. / Kumarasingha, R. / Mehmood, S. / Donnellan, F.R. / Minkah, N.K. / Dadonaite, B. / Diouf, A. / Galaway, F. / Silk, S.E. / Jamwal, A. / Marshall, J.M. / Miura, K. / Foquet, L. / Elias, S.C. / Labbe, G.M. / Douglas, A.D. / Jin, J. / Payne, R.O. / Illingworth, J.J. / Pattinson, D.J. / Pulido, D. / Williams, B.G. / de Jongh, W.A. / Wright, G.J. / Kappe, S.H.I. / Robinson, C.V. / Long, C.A. / Crabb, B.S. / Gilson, P.R. / Higgins, M.K. / Draper, S.J.
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev / database_PDB_rev_record
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: R5.004 heavy chain
B: R5.004 light chain
C: R5.004 heavy chain
D: R5.004 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,02211
Polymers95,4104
Non-polymers6127
Water12,340685
1
A: R5.004 heavy chain
B: R5.004 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7973
Polymers47,7052
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-22 kcal/mol
Surface area20200 Å2
MethodPISA
2
C: R5.004 heavy chain
D: R5.004 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2258
Polymers47,7052
Non-polymers5206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-29 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.210, 70.180, 73.260
Angle α, β, γ (deg.)101.42, 92.97, 112.47
Int Tables number1
Space group name H-MP1

-
Components

#1: Antibody R5.004 heavy chain


Mass: 24651.633 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 R5.004 light chain


Mass: 23053.365 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 685 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M NaAc pH 4.5, 30% PEG 8000 0.33% hexamminecobalt(III) chloride, 0.06 M MES monohydrate, 0.06 PIPES, 0.02 M HEPES chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.66→42.45 Å / Num. obs: 111530 / % possible obs: 95.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 32.53 Å2 / Net I/σ(I): 8.6
Reflection shellResolution: 1.66→1.69 Å / Num. unique obs: 5493

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→42.45 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.092 / SU Rfree Blow DPI: 0.088 / SU Rfree Cruickshank DPI: 0.087
RfactorNum. reflection% reflectionSelection details
Rfree0.204 5400 4.84 %RANDOM
Rwork0.183 ---
obs0.184 111520 95.7 %-
Displacement parametersBiso mean: 45.29 Å2
Baniso -1Baniso -2Baniso -3
1--3.354 Å28.1444 Å26.7456 Å2
2--4.0693 Å22.4361 Å2
3----0.7153 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 1.66→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6452 0 40 685 7177
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016666HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.099091HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2142SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1103HARMONIC5
X-RAY DIFFRACTIONt_it6666HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.85
X-RAY DIFFRACTIONt_other_torsion16.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion904SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7633SEMIHARMONIC4
LS refinement shellResolution: 1.66→1.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 407 5 %
Rwork0.2279 7741 -
all0.2278 8148 -
obs--94.58 %
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)
11.76431.81371.50141.9481.95991.56380.096-0.09160.17370.0657-0.17870.2060.1141-0.21320.0827-0.0657-0.0927-0.0493-0.06410.0411-0.1453-39.146524.670612.0495
21.21911.24491.48211.21771.80641.5184-0.24070.2228-0.03-0.28240.2474-0.0074-0.36640.3286-0.00670.0366-0.1078-0.014-0.04790.0133-0.1621-29.92426.6066-2.5668
31.03141.00720.04481.20860.0690.02850.0264-0.08130.03130.132-0.0125-0.01460.02680.0018-0.0139-0.0740.0153-0.0181-0.129-0.0175-0.0982-59.319146.822541.5261
41.79261.14560.39630.63840.21810.20690.00260.0946-0.3028-0.04320.0508-0.19270.01950.0062-0.0534-0.11820.0228-0.0036-0.1431-0.0257-0.0358-47.16835.466438.2025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

+
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://pdbjlvh1.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