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- PDB-9hi5: Structure of scaffold FI6-focused design_02 -

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Basic information

Entry
Database: PDB / ID: 9hi5
TitleStructure of scaffold FI6-focused design_02
ComponentsGDSL-like protein
KeywordsBIOSYNTHETIC PROTEIN / scaffold / influenza
Function / homology: / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / ISOPROPYL ALCOHOL / GDSL-like protein
Function and homology information
Biological speciesBacteroides uniformis ATCC 8492 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsCramer, J.T. / Krey, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Structure of scaffold FI6-focused design_02
Authors: Cramer, J.T. / Krey, T.
History
DepositionNov 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDSL-like protein
B: GDSL-like protein
C: GDSL-like protein
D: GDSL-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6555
Polymers98,5954
Non-polymers601
Water11,980665
1
A: GDSL-like protein
B: GDSL-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3583
Polymers49,2982
Non-polymers601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-3 kcal/mol
Surface area18480 Å2
MethodPISA
2
C: GDSL-like protein
D: GDSL-like protein


Theoretical massNumber of molelcules
Total (without water)49,2982
Polymers49,2982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-10 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.050, 63.310, 98.180
Angle α, β, γ (deg.)96.360, 99.530, 114.570
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
GDSL-like protein


Mass: 24648.803 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis ATCC 8492 (bacteria)
Gene: BACUNI_03406 / Production host: Escherichia coli (E. coli) / References: UniProt: A7V743
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 20% (w/V) PEG 4,000, 15% (V/V) 2-Propanol, 100mM Sodium citrate pH 5,5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→43.48 Å / Num. obs: 153486 / % possible obs: 93.6 % / Redundancy: 1.83 % / Biso Wilson estimate: 37.322 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.07 / Χ2: 0.991 / Net I/σ(I): 8.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.951.8290.5241.29111360.6120.74191.8
1.95-21.8750.411.77111140.6940.5893.7
2-2.061.860.3272.23108670.7760.46294.2
2.06-2.121.8320.2452.95105440.8710.34694.4
2.12-2.191.7670.193.54101210.9180.26993.8
2.19-2.271.7890.1634.2298340.9310.2394.1
2.27-2.361.8880.1345.2494300.9550.1993.2
2.36-2.451.8680.1195.7991570.9650.16994
2.45-2.561.8290.1036.7187420.9720.14693.8
2.56-2.691.7310.087.8683520.9830.11394.1
2.69-2.831.8410.0719.679620.9840.193.9
2.83-31.8860.05612.0575310.9910.07994.1
3-3.211.8490.04414.5770790.9940.06394.3
3.21-3.471.750.03617.2466270.9950.05193.9
3.47-3.81.8190.0320.860570.9960.04293.6
3.8-4.251.8840.02723.6554270.9970.03893.8
4.25-4.91.8160.02524.5547680.9970.03591.8
4.9-6.011.7780.02623.0740210.9970.03793.5
6.01-8.491.8820.02524.9530650.9970.03691.1
8.49-43.481.7490.02229.9816520.9980.03190.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.33 Å45.46 Å
Translation5.33 Å45.46 Å

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.1phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IYJ

4iyj


Resolution: 1.9→43.48 Å / SU ML: 0.2026 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.4287
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2018 3976 5 %
Rwork0.1707 75573 -
obs0.1722 79549 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.13 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6167 0 4 665 6836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01016314
X-RAY DIFFRACTIONf_angle_d0.97428592
X-RAY DIFFRACTIONf_chiral_restr0.0686976
X-RAY DIFFRACTIONf_plane_restr0.01161127
X-RAY DIFFRACTIONf_dihedral_angle_d5.5335880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.30791360.29022587X-RAY DIFFRACTION92.68
1.92-1.950.30721410.2762678X-RAY DIFFRACTION95.95
1.95-1.970.2841420.24222724X-RAY DIFFRACTION96.69
1.97-20.26871390.23962629X-RAY DIFFRACTION96.35
2-2.030.24621410.21972683X-RAY DIFFRACTION96.65
2.03-2.060.22071440.21572730X-RAY DIFFRACTION97.06
2.06-2.090.23481410.19482683X-RAY DIFFRACTION96.94
2.09-2.120.22441420.19072709X-RAY DIFFRACTION96.97
2.12-2.160.20171380.18772630X-RAY DIFFRACTION96.88
2.16-2.20.23071440.18392739X-RAY DIFFRACTION97.17
2.2-2.240.24671420.18742692X-RAY DIFFRACTION97.12
2.24-2.290.19691420.17992699X-RAY DIFFRACTION96.14
2.29-2.340.2341420.18122706X-RAY DIFFRACTION96.97
2.34-2.390.20651410.17392664X-RAY DIFFRACTION97.4
2.39-2.450.21991440.1752747X-RAY DIFFRACTION97.7
2.45-2.520.21841410.17462668X-RAY DIFFRACTION97
2.52-2.590.19611430.17272729X-RAY DIFFRACTION97.59
2.59-2.680.20061430.1742708X-RAY DIFFRACTION97.8
2.68-2.770.21031440.17922730X-RAY DIFFRACTION97.92
2.77-2.880.22591450.17792749X-RAY DIFFRACTION97.84
2.88-3.010.20831410.17612683X-RAY DIFFRACTION97.82
3.01-3.170.2071430.17182722X-RAY DIFFRACTION97.75
3.17-3.370.18091420.17142707X-RAY DIFFRACTION97.94
3.37-3.630.19961450.16532740X-RAY DIFFRACTION97.66
3.63-40.18361430.15222719X-RAY DIFFRACTION98.25
4-4.580.16551430.13582722X-RAY DIFFRACTION97.71
4.58-5.760.18161430.15522711X-RAY DIFFRACTION97.24
5.76-43.480.17991410.15262685X-RAY DIFFRACTION96.71
Refinement TLS params.Method: refined / Origin x: -26.397972327 Å / Origin y: 47.0743295081 Å / Origin z: 26.7810177968 Å
111213212223313233
T0.139163115007 Å20.0100691855104 Å2-0.0208194004007 Å2-0.200703634802 Å2-0.0121497598229 Å2--0.206800182417 Å2
L0.309676357029 °20.125673452901 °2-0.165697051475 °2-0.490714537563 °2-0.307584531516 °2--0.96269724809 °2
S0.0400077407554 Å °-0.0698239525199 Å °-0.0265189602091 Å °0.0954609835307 Å °-0.0383448808879 Å °0.00892467380594 Å °-0.0788529550858 Å °-0.0367534423595 Å °-0.00671624373243 Å °
Refinement TLS groupSelection details: all

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