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- PDB-7kbo: Reverse Transcriptase Diabody with S82bC, R83T Mutations Crystall... -

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Basic information

Entry
Database: PDB / ID: 7kbo
TitleReverse Transcriptase Diabody with S82bC, R83T Mutations Crystallized in C2
ComponentsSingle-chain scFv
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: 2.2 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
DepositionOct 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2Oct 18, 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 1.3Oct 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

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Assembly

Deposited unit
A: Single-chain scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6655
Polymers26,4171
Non-polymers2484
Water1,928107
1
A: Single-chain scFv
hetero molecules

A: Single-chain scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,33110
Polymers52,8342
Non-polymers4978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5120 Å2
ΔGint-20 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.707, 86.018, 36.682
Angle α, β, γ (deg.)90.000, 117.983, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

21A-471-

HOH

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Components

#1: Antibody Single-chain scFv


Mass: 26417.219 Da / Num. of mol.: 1 / Mutation: S82bC, R83T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: scFv / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 1.94 Å3/Da / Density % sol: 36.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 6% v/v Propanol, 0.1 M sodium acetate trihydrate pH 4.5, 26 % PEG 550 MME

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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: 2.2→50 Å / Num. obs: 10076 / % possible obs: 97.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 28.38 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.047 / Net I/σ(I): 27.8
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.107 / Num. unique obs: 493 / CC1/2: 0.989 / Rrim(I) all: 0.128 / % possible all: 96.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXphasing
PHENIXv1.14-3260refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VRP

6vrp


Resolution: 2.2→33.73 Å / SU ML: 0.2497 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 24.7842 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2253 481 4.93 %
Rwork0.1776 9270 -
obs0.18 9751 94.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.18 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 16 107 1813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271742
X-RAY DIFFRACTIONf_angle_d0.60862365
X-RAY DIFFRACTIONf_chiral_restr0.0449262
X-RAY DIFFRACTIONf_plane_restr0.0032300
X-RAY DIFFRACTIONf_dihedral_angle_d2.6468996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.510.2911520.20282831X-RAY DIFFRACTION87.3
2.51-3.170.2751630.1993197X-RAY DIFFRACTION97.79
3.17-33.730.18371660.16083242X-RAY DIFFRACTION97.99

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