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- PDB-6vun: Reverse Transcriptase Diabody with R83C Mutation -

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Basic information

Entry
Database: PDB / ID: 6vun
TitleReverse Transcriptase Diabody with R83C Mutation
ComponentsSingle-chain Fv
KeywordsPROTEIN BINDING / Antibody fragment
Function / homologyCITRATE ANION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChesterman, C. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37 AI027690 United States
CitationJournal: Structure / Year: 2021
Title: Co-crystallization with diabodies: A case study for the introduction of synthetic symmetry.
Authors: Chesterman, C. / Arnold, E.
History
DepositionFeb 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 16, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 11, 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
A: Single-chain Fv
B: Single-chain Fv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,60812
Polymers50,8602
Non-polymers74810
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-15 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.089, 56.632, 161.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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

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Components

#1: Antibody Single-chain Fv


Mass: 25430.182 Da / Num. of mol.: 2 / Mutation: R83C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14% v/v Propanol, 0.1 M Sodium citrate dibasic dehydrate pH 5.0, 10% w/v PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 170553 / % possible obs: 99.6 % / Redundancy: 8.9 % / Biso Wilson estimate: 12.48 Å2 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.055 / Net I/σ(I): 44
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.617 / Num. unique obs: 4903 / Rrim(I) all: 0.661 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VRP

6vrp


Resolution: 1.4→45.542 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1671 3502 2.05 %
Rwork0.1379 --
obs0.1385 170553 88.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→45.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 0 49 516 4047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063893
X-RAY DIFFRACTIONf_angle_d0.9495344
X-RAY DIFFRACTIONf_dihedral_angle_d17.4421366
X-RAY DIFFRACTIONf_chiral_restr0.077584
X-RAY DIFFRACTIONf_plane_restr0.005699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41880.2281600.1872965X-RAY DIFFRACTION39
1.4188-1.43910.2227820.16673638X-RAY DIFFRACTION48
1.4391-1.46050.2053920.15714223X-RAY DIFFRACTION56
1.4605-1.48340.1832980.14884770X-RAY DIFFRACTION63
1.4834-1.50770.18751090.1455322X-RAY DIFFRACTION71
1.5077-1.53370.19721300.13755998X-RAY DIFFRACTION79
1.5337-1.56160.18421420.12986184X-RAY DIFFRACTION83
1.5616-1.59160.16961310.12256568X-RAY DIFFRACTION87
1.5916-1.62410.15551570.12247078X-RAY DIFFRACTION94
1.6241-1.65940.16081560.12567370X-RAY DIFFRACTION97
1.6594-1.6980.18411460.12517498X-RAY DIFFRACTION99
1.698-1.74050.12811630.1237508X-RAY DIFFRACTION99
1.7405-1.78750.19261520.12257508X-RAY DIFFRACTION100
1.7875-1.84010.14381660.12687554X-RAY DIFFRACTION99
1.8401-1.89950.1821440.1277505X-RAY DIFFRACTION100
1.8995-1.96740.15681650.12427590X-RAY DIFFRACTION100
1.9674-2.04620.14441650.12337477X-RAY DIFFRACTION100
2.0462-2.13930.16211580.12147550X-RAY DIFFRACTION100
2.1393-2.25210.1541560.12397581X-RAY DIFFRACTION100
2.2521-2.39320.13911610.12787440X-RAY DIFFRACTION99
2.3932-2.5780.16481570.13037553X-RAY DIFFRACTION100
2.578-2.83740.16941620.13787555X-RAY DIFFRACTION100
2.8374-3.24780.14951500.14727536X-RAY DIFFRACTION100
3.2478-4.09150.19121570.15137541X-RAY DIFFRACTION100
4.0915-45.5420.18161430.16417539X-RAY DIFFRACTION100

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