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- PDB-7kbm: Reverse Transcriptase Diabody with R83C Mutation Crystallized in C2 -

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Basic information

Entry
Database: PDB / ID: 7kbm
TitleReverse Transcriptase Diabody with R83C Mutation 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 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 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Single-chain scFv


Theoretical massNumber of molelcules
Total (without water)26,4031
Polymers26,4031
Non-polymers00
Water2,576143
1
A: Single-chain scFv

A: Single-chain scFv


Theoretical massNumber of molelcules
Total (without water)52,8062
Polymers52,8062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4450 Å2
ΔGint-28 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.638, 86.302, 36.249
Angle α, β, γ (deg.)90.000, 116.500, 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-366-

HOH

21A-397-

HOH

31A-442-

HOH

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Components

#1: Antibody Single-chain scFv


Mass: 26403.193 Da / Num. of mol.: 1 / Mutation: R83C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: scFv / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
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: 1.95 Å3/Da / Density % sol: 36.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Sodium acetate trihydrate pH 4.5, 30% PEG 300

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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→50 Å / Num. obs: 13604 / % possible obs: 98.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 23.19 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.12 / Net I/σ(I): 11.6
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.347 / Num. unique obs: 669 / CC1/2: 0.881 / Rrim(I) all: 0.417 / % possible all: 97.5

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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→33.38 Å / SU ML: 0.3242 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 30.3003 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2574 630 5.07 %
Rwork0.2089 11791 -
obs0.2114 12421 89.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.53 Å2
Refinement stepCycle: LAST / Resolution: 2→33.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 0 143 1843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211780
X-RAY DIFFRACTIONf_angle_d0.53652436
X-RAY DIFFRACTIONf_chiral_restr0.0421268
X-RAY DIFFRACTIONf_plane_restr0.0031317
X-RAY DIFFRACTIONf_dihedral_angle_d2.22681351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.150.3565900.28491746X-RAY DIFFRACTION66.69
2.15-2.360.33091200.2682288X-RAY DIFFRACTION86.87
2.36-2.710.28481350.24432547X-RAY DIFFRACTION97.24
2.71-3.410.28151440.20622589X-RAY DIFFRACTION98.56
3.41-33.380.20041410.17042621X-RAY DIFFRACTION98.26

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