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- PDB-6w3f: Rd1NTF2_05_I64F_A80G_T94P_D101K_L106W -

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Basic information

Entry
Database: PDB / ID: 6w3f
TitleRd1NTF2_05_I64F_A80G_T94P_D101K_L106W
ComponentsRd1NTF2_05_I64F_A80G_T94P_D101K_L106W
KeywordsBIOSYNTHETIC PROTEIN / NTF2-like / synthetic
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å
AuthorsBick, M.J. / Basanta, B. / Sankaran, B. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)Synergistic Discovery and Design (SD2) HR0011835403 contract FA8750-17-C-0219 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: An enumerative algorithm for de novo design of proteins with diverse pocket structures.
Authors: Basanta, B. / Bick, M.J. / Bera, A.K. / Norn, C. / Chow, C.M. / Carter, L.P. / Goreshnik, I. / Dimaio, F. / Baker, D.
History
DepositionMar 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 23, 2021Group: Structure summary / Category: audit_author
Revision 1.4Mar 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 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rd1NTF2_05_I64F_A80G_T94P_D101K_L106W
B: Rd1NTF2_05_I64F_A80G_T94P_D101K_L106W


Theoretical massNumber of molelcules
Total (without water)26,9552
Polymers26,9552
Non-polymers00
Water99155
1
A: Rd1NTF2_05_I64F_A80G_T94P_D101K_L106W


Theoretical massNumber of molelcules
Total (without water)13,4771
Polymers13,4771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rd1NTF2_05_I64F_A80G_T94P_D101K_L106W


Theoretical massNumber of molelcules
Total (without water)13,4771
Polymers13,4771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.510, 38.510, 134.148
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Rd1NTF2_05_I64F_A80G_T94P_D101K_L106W


Mass: 13477.491 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution concentration: 7.7mg/mL diluted 1:1 in 0.09M Sodium nitrate, 0.09 Sodium phosphate dibasic, 0.09M Ammonium sulfate, pH 6.5 0.1M Imidazole/MES monohydrate (acid), %50v/v of ...Details: Protein solution concentration: 7.7mg/mL diluted 1:1 in 0.09M Sodium nitrate, 0.09 Sodium phosphate dibasic, 0.09M Ammonium sulfate, pH 6.5 0.1M Imidazole/MES monohydrate (acid), %50v/v of 40% v/v PEG 500 MME; 20 % w/v PEG 20000 (Morpheus-HT96 C1)

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen cryo stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.978633 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2018
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978633 Å / Relative weight: 1
ReflectionResolution: 1.83→44.72 Å / Num. obs: 19640 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 29.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.036 / Rrim(I) all: 0.075 / Net I/σ(I): 10.7 / Num. measured all: 81919 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.83-1.874.22.455486411710.4121.3882.8270.6100
8.97-44.724.10.0227211750.9990.0120.02544.299

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.44 Å44.72 Å
Translation2.44 Å44.72 Å

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHASER2.8.2phasing
PHENIXdev-3112refinement
PDB_EXTRACT3.25data extraction
XDSJun 17, 2015data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational design model

Resolution: 1.83→44.716 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 33
RfactorNum. reflection% reflection
Rfree0.2551 1702 9.81 %
Rwork0.2162 --
obs0.22 17345 88.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.16 Å2 / Biso mean: 52.8598 Å2 / Biso min: 23.78 Å2
Refinement stepCycle: final / Resolution: 1.83→44.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 0 55 1770
Biso mean---43.69 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071744
X-RAY DIFFRACTIONf_angle_d0.8372354
X-RAY DIFFRACTIONf_dihedral_angle_d10.2711048
X-RAY DIFFRACTIONf_chiral_restr0.053266
X-RAY DIFFRACTIONf_plane_restr0.005309
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8303-1.88410.42861010.387295066
1.8841-1.94490.37761160.3461109873
1.9449-2.01450.33021350.3024116879
2.0145-2.09510.33331340.2836120984
2.0951-2.19050.30241350.2567129388
2.1905-2.3060.3151460.2372134990
2.306-2.45040.27191380.2465136092
2.4504-2.63960.26951520.2474139395
2.6396-2.90520.30371670.2492145297
2.9052-3.32550.27211500.222144099
3.3255-4.18920.22421680.1771147099
4.1892-44.7160.20421600.1807146199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.95720.4954-0.07470.2563-0.0072.6723-0.01550.1559-0.0573-0.0551-0.2840.46020.2718-0.58310.33560.31950.11530.11330.33530.06220.3604-11.224225.902886.2429
22.6378-2.0890.52771.7989-0.19520.6690.2086-0.5002-0.14090.1319-0.01520.3668-0.106-0.36010.04330.43990.06250.05430.38320.0290.3476-5.39631.916998.5906
31.17671.8017-2.12694.2129-5.65399.0452-0.3357-0.09110.46620.01570.053-0.4182-0.60390.78270.2240.7329-0.0323-0.0050.35740.08980.37436.146238.601293.1899
44.0166-1.02891.42425.3421-1.88311.59540.117-0.29940.65230.557-0.0384-0.4702-0.6166-0.70970.03370.70690.19950.01230.3686-0.08140.4003-4.12140.486295.8315
51.4833-0.96450.00241.0256-0.47211.1090.0302-0.1240.31750.14570.016-0.22890.00450.22-0.00280.46160.2060.0520.32150.04110.3403-3.239130.086981.7112
60.7376-0.09810.18125.2031-1.4941.4116-0.08490.04970.06480.18740.2171-0.0911-0.0955-0.29520.06610.37650.11590.0920.34570.03940.3229-2.232633.655684.0603
73.05910.90960.31065.9429-1.252.9376-0.0218-0.22850.19630.5207-0.0572-0.1622-0.3475-0.25650.07340.45930.07890.09380.33060.05530.296-0.619727.62491.7726
82.1706-0.82960.44482.04931.63623.6705-0.47340.05720.19890.50140.25370.44850.0848-0.60010.27250.45650.01940.13010.29380.04540.466-11.962813.854772.7476
91.90530.4221-0.78191.9346-1.32081.0362-0.01970.6255-0.0381-0.1762-0.0473-0.02690.8661-0.1897-0.06310.6086-0.01540.06450.3467-0.06890.2808-3.25437.012860.2393
104.27413.02481.11063.5216-0.37481.2694-0.37980.3623-0.5023-0.44250.5035-0.10860.38250.16170.87950.58950.0920.11550.1942-0.00820.3472-4.79417.158269.6251
112.5840.16890.52252.69750.72851.3433-0.4098-0.122-0.27650.55180.2380.16350.2398-0.26810.08670.48690.14650.18070.29060.05380.325-1.511710.298872.1857
122.40561.1571-0.33021.47210.81472.0711-0.22480.40810.206-0.3902-0.0638-0.10290.63390.13160.15890.3580.0548-0.00240.3339-0.03640.3112-2.588213.877464.7207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 19 )A0 - 19
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 33 )A20 - 33
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 44 )A34 - 44
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 58 )A45 - 58
5X-RAY DIFFRACTION5chain 'A' and (resid 59 through 86 )A59 - 86
6X-RAY DIFFRACTION6chain 'A' and (resid 87 through 102 )A87 - 102
7X-RAY DIFFRACTION7chain 'A' and (resid 103 through 114 )A103 - 114
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 19 )B1 - 19
9X-RAY DIFFRACTION9chain 'B' and (resid 20 through 44 )B20 - 44
10X-RAY DIFFRACTION10chain 'B' and (resid 45 through 72 )B45 - 72
11X-RAY DIFFRACTION11chain 'B' and (resid 73 through 102 )B73 - 102
12X-RAY DIFFRACTION12chain 'B' and (resid 103 through 114 )B103 - 114

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