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- PDB-6w70: Crystal Structure of apixaban-bound ABLE -

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Basic information

Entry
Database: PDB / ID: 6w70
TitleCrystal Structure of apixaban-bound ABLE
ComponentsDe novo designed ABLE
KeywordsDE NOVO PROTEIN / 4-helix bundle / de novo / ligand-binding
Function / homologyACETATE ION / Chem-GG2
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.296 Å
AuthorsPolizzi, N.F.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
CitationJournal: Science / Year: 2020
Title: A defined structural unit enables de novo design of small-molecule-binding proteins.
Authors: Polizzi, N.F. / DeGrado, W.F.
History
DepositionMar 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed ABLE
C: De novo designed ABLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7687
Polymers27,6352
Non-polymers1,1335
Water4,900272
1
A: De novo designed ABLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4915
Polymers13,8171
Non-polymers6744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: De novo designed ABLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2772
Polymers13,8171
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.194, 78.445, 43.133
Angle α, β, γ (deg.)90.000, 106.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein De novo designed ABLE


Mass: 13817.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GG2 / 1-(4-METHOXYPHENYL)-7-OXO-6-[4-(2-OXOPIPERIDIN-1-YL)PHENYL]-4,5,6,7-TETRAHYDRO-1H-PYRAZOLO[3,4-C]PYRIDINE-3-CARBOXAMIDE / Apixaban


Mass: 459.497 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H25N5O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, anticoagulant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.6 M AmSO4, 0.1 M Na acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.292→41.259 Å / Num. all: 54993 / Num. obs: 54993 / % possible obs: 97.5 % / Redundancy: 10.7 % / Rpim(I) all: 0.037 / Rrim(I) all: 0.124 / Rsym value: 0.111 / Net I/av σ(I): 3.3 / Net I/σ(I): 27.9 / Num. measured all: 587522
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.292-1.3540.5951.167980.3680.7910.59582.6
1.35-1.449.60.4671.477720.1730.5310.467100
1.44-1.5411.90.3311.972900.1090.370.331100
1.54-1.6612.30.272.468240.0870.30.27100
1.66-1.8212.30.211362590.0670.2330.211100
1.82-2.0311.30.1414.456650.0480.1610.141100
2.03-2.3512.80.102650190.0320.1150.102100
2.35-2.8712.50.0847.142400.0260.0940.084100
2.87-4.06110.0886.532790.030.10.088100
4.06-41.25911.40.0945.918470.030.1040.094100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Designed model

Resolution: 1.296→41.259 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1832 2702 4.92 %
Rwork0.1605 52174 -
obs0.1616 54876 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.41 Å2 / Biso mean: 20.1028 Å2 / Biso min: 8.59 Å2
Refinement stepCycle: final / Resolution: 1.296→41.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 137 272 2309
Biso mean--18.38 27.55 -
Num. residues----252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.296-1.31910.52361230.5274223280
1.3191-1.34440.36861570.3805270097
1.3444-1.37190.31071430.26812701100
1.3719-1.40170.26531410.18522797100
1.4017-1.43430.23251470.17022759100
1.4343-1.47020.1871370.16112793100
1.4702-1.510.20641260.15612764100
1.51-1.55440.19531640.15462735100
1.5544-1.60460.18821450.15162807100
1.6046-1.66190.20591360.14472789100
1.6619-1.72840.18941390.14832756100
1.7284-1.80710.19651420.14772774100
1.8071-1.90240.19811420.15192781100
1.9024-2.02160.17521500.14772759100
2.0216-2.17770.1611520.14642801100
2.1777-2.39680.17561460.13582780100
2.3968-2.74350.14781370.14632788100
2.7435-3.45630.1611390.15872808100
3.4563-41.2590.16271360.16192850100

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