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Basic information

Entry
Database: PDB / ID: 6w3g
TitleRd1NTF2_04 with long sheet
ComponentsRd1NTF2_04
KeywordsBIOSYNTHETIC PROTEIN / NTF2-like / synthetic
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 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_04
B: Rd1NTF2_04


Theoretical massNumber of molelcules
Total (without water)27,7972
Polymers27,7972
Non-polymers00
Water1,856103
1
A: Rd1NTF2_04


Theoretical massNumber of molelcules
Total (without water)13,8991
Polymers13,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rd1NTF2_04


Theoretical massNumber of molelcules
Total (without water)13,8991
Polymers13,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.578, 36.814, 177.303
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Rd1NTF2_04


Mass: 13898.522 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.: 103 / 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: 1.91 Å3/Da / Density % sol: 35.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution concentration: 48.7mg/mL diluted 1:1 in 0.12M 1,6-Hexanediol; 0.12M 1-Butanol; 0.12M 1,2-Propanediol; 0.12M 2- Propanol; 0.12M 1,4-Butanediol; 0.12M 1,3-Propanediol, 0.1M ...Details: Protein solution concentration: 48.7mg/mL diluted 1:1 in 0.12M 1,6-Hexanediol; 0.12M 1-Butanol; 0.12M 1,2-Propanediol; 0.12M 2- Propanol; 0.12M 1,4-Butanediol; 0.12M 1,3-Propanediol, 0.1M Imidazole/MES monohydrate (acid), pH 6.5, and 50% v/v of 40% v/v PEG 500 MME; 20 % w/v PEG 20000

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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: 0.999989 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2018
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999989 Å / Relative weight: 1
ReflectionResolution: 1.62→44.33 Å / Num. obs: 28154 / % possible obs: 99.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 25.13 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.02 / Rrim(I) all: 0.045 / Net I/σ(I): 18.5 / Num. measured all: 132988
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
1.62-1.654.81.864653813610.2410.9342.0920.999.9
8.87-44.333.50.0147472130.9990.0080.01761.295.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.41 Å44.33 Å
Translation2.41 Å44.33 Å

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASER2.8.2phasing
PHENIXdev-3084refinement
PDB_EXTRACT3.25data extraction
XDSJun 17, 2015data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational design model

Resolution: 1.62→44.326 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.88
RfactorNum. reflection% reflection
Rfree0.2399 1897 7.19 %
Rwork0.2109 --
obs0.213 26376 93.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.77 Å2 / Biso mean: 45.3642 Å2 / Biso min: 16.44 Å2
Refinement stepCycle: final / Resolution: 1.62→44.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 0 103 1789
Biso mean---44.71 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051816
X-RAY DIFFRACTIONf_angle_d0.6312465
X-RAY DIFFRACTIONf_dihedral_angle_d15.3641089
X-RAY DIFFRACTIONf_chiral_restr0.055270
X-RAY DIFFRACTIONf_plane_restr0.004325
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6201-1.66060.35711100.3668141778
1.6606-1.70550.33521180.3494153884
1.7055-1.75570.32871280.3341155185
1.7557-1.81240.34311240.2973163589
1.8124-1.87720.28651320.2638165491
1.8772-1.95230.23721380.239175195
1.9523-2.04120.27041380.2175180196
2.0412-2.14880.25491380.2127179698
2.1488-2.28340.25491400.216181598
2.2834-2.45970.22931440.2112185899
2.4597-2.70720.24621420.2104186299
2.7072-3.09890.28691450.2113187999
3.0989-3.90390.20171440.18971897100
3.9039-44.3260.21111560.1886202598
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)
10.19770.0417-0.2690.58810.10550.3150.0547-0.13560.17450.3379-0.0353-0.2506-0.28050.18130.01260.3263-0.05670.03820.2584-0.02460.32914.347417.613458.8381
20.24640.1518-0.05620.15760.09330.20920.1192-0.0646-0.6458-0.2799-0.22530.0816-0.0215-0.3925-0.00210.32810.05450.05160.23370.03730.25479.91791.503758.4056
30.36790.38140.22160.25040.16380.36340.0293-0.4611-0.25030.2877-0.0712-0.1847-0.05640.25810.00820.2912-0.0271-0.00890.34320.08250.292119.17926.835462.9552
40.3346-0.2782-0.35570.2360.03840.0509-0.08760.34970.55640.08340.0287-0.3296-0.09850.0949-0.00420.1596-0.00970.0070.2190.0260.313117.659314.107248.3072
50.4939-0.3189-0.1417-0.11710.18880.3931-0.1823-0.04060.30140.24390.2444-0.1865-0.01210.00420.00860.18940.02820.010.1945-0.01490.294815.405410.220249.5768
60.77680.55020.8480.4010.56030.8943-0.0818-0.34560.19-0.0089-0.0740.0832-0.3583-0.1744-0.13470.23660.02410.03750.20770.02140.20037.176411.202455.2971
70.0083-0.00440.03710.06510.20130.9835-0.15170.3066-0.30650.7441-0.15730.1170.81581.139-0.00050.4108-0.07220.02170.7577-0.0640.3815-7.5321-7.803177.6994
81.4827-0.09330.72660.40890.20161.12630.23890.3803-0.64060.05880.1241-0.0265-0.43830.22540.3340.3208-0.3966-0.17451.25920.0930.4241-6.6478-5.174768.4454
90.61480.07250.01460.1755-0.03850.20510.1775-0.22050.132-0.1343-0.0785-0.0865-0.00280.14470.39030.3217-0.03110.01340.42540.16690.25616.82860.219172.0281
100.3516-0.03240.26020.41520.18220.21670.19720.5936-0.4316-1.1433-0.10520.26710.6129-0.0931-0.01330.5183-0.1427-0.01170.35530.00270.3763.5462-8.968368.3224
111.32840.1838-0.1310.4223-0.1510.47690.08790.1845-0.2694-0.04480.12140.7845-0.112-0.06730.06040.3621-0.03180.03450.29720.06040.2857-0.4813-8.399483.7052
120.50750.3925-0.26670.7957-0.04880.36390.02030.143-0.1190.09030.1575-0.10460.13060.04830.18090.39370.0297-0.01440.34970.06630.25814.4586-10.073482.826
130.50380.13250.11390.95620.65890.5855-0.2642-0.03630.06320.13360.6002-0.0637-0.393-0.29290.26590.32070.0051-0.01340.35530.20280.30490.59350.93778.0141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 33 )A4 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 44 )A34 - 44
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 58 )A45 - 58
4X-RAY DIFFRACTION4chain 'A' and (resid 59 through 72 )A59 - 72
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 102 )A73 - 102
6X-RAY DIFFRACTION6chain 'A' and (resid 104 through 114 )A104 - 114
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 19 )B5 - 19
8X-RAY DIFFRACTION8chain 'B' and (resid 20 through 28 )B20 - 28
9X-RAY DIFFRACTION9chain 'B' and (resid 29 through 44 )B29 - 44
10X-RAY DIFFRACTION10chain 'B' and (resid 45 through 58 )B45 - 58
11X-RAY DIFFRACTION11chain 'B' and (resid 59 through 86 )B59 - 86
12X-RAY DIFFRACTION12chain 'B' and (resid 87 through 100 )B87 - 100
13X-RAY DIFFRACTION13chain 'B' and (resid 101 through 114 )B101 - 114

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