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- PDB-6vrp: Reverse Transcriptase Diabody with R83T Mutation -

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Basic information

Entry
Database: PDB / ID: 6vrp
TitleReverse Transcriptase Diabody with R83T Mutation
ComponentsSingle-chain Fv
KeywordsPROTEIN BINDING / diabody / immunoglobin / reverse transcriptase
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 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
Revision 1.4Oct 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

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Assembly

Deposited unit
A: Single-chain Fv
B: Single-chain Fv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,47424
Polymers52,8022
Non-polymers1,67122
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-110 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.728, 55.460, 157.304
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

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Components

#1: Antibody Single-chain Fv


Mass: 26401.154 Da / Num. of mol.: 2
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.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M Ammonium Sulfate, 20% PEG 3350

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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 S 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: 1.6→50 Å / Num. obs: 61848 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 12.65 Å2 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.05 / Net I/σ(I): 39.14
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.368 / Num. unique obs: 3029 / Rrim(I) all: 0.398 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X4X

4x4x


Resolution: 1.6→43.8 Å / SU ML: 0.1224 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.4797 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1827 1609 2.61 %
Rwork0.1464 60118 -
obs0.1474 61727 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 97 441 3988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393842
X-RAY DIFFRACTIONf_angle_d0.75075259
X-RAY DIFFRACTIONf_chiral_restr0.0492573
X-RAY DIFFRACTIONf_plane_restr0.0036674
X-RAY DIFFRACTIONf_dihedral_angle_d15.21781339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.22141450.14715359X-RAY DIFFRACTION99.51
1.65-1.710.21891470.14485383X-RAY DIFFRACTION99.87
1.71-1.780.20761460.13255399X-RAY DIFFRACTION99.82
1.78-1.860.16321320.12875406X-RAY DIFFRACTION99.77
1.86-1.960.18751470.12455414X-RAY DIFFRACTION99.91
1.96-2.080.15171490.135420X-RAY DIFFRACTION100
2.08-2.240.15981440.13255452X-RAY DIFFRACTION100
2.24-2.470.18531490.14575462X-RAY DIFFRACTION99.88
2.47-2.820.17611490.14845484X-RAY DIFFRACTION99.95
2.82-3.560.19691410.15215551X-RAY DIFFRACTION99.91
3.56-43.80.1811600.16565788X-RAY DIFFRACTION99.9

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