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- PDB-3u3b: Crystal Structure of Computationally Redesigned Four-Helix Bundle -

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Basic information

Entry
Database: PDB / ID: 3u3b
TitleCrystal Structure of Computationally Redesigned Four-Helix Bundle
Componentscomputationally designed four-helix bundle protein
KeywordsUNKNOWN FUNCTION / Four-Helix Bundle / Flexible Backbone Protein Design / hyperthermostable
Function / homologyHPT domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.854 Å
AuthorsMurphy, G.S. / Machius, M.
CitationJournal: Structure / Year: 2012
Title: Increasing sequence diversity with flexible backbone protein design: the complete redesign of a protein hydrophobic core.
Authors: Murphy, G.S. / Mills, J.L. / Miley, M.J. / Machius, M. / Szyperski, T. / Kuhlman, B.
History
DepositionOct 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 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 1.4Apr 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: computationally designed four-helix bundle protein
B: computationally designed four-helix bundle protein


Theoretical massNumber of molelcules
Total (without water)26,5332
Polymers26,5332
Non-polymers00
Water2,522140
1
A: computationally designed four-helix bundle protein


Theoretical massNumber of molelcules
Total (without water)13,2661
Polymers13,2661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: computationally designed four-helix bundle protein


Theoretical massNumber of molelcules
Total (without water)13,2661
Polymers13,2661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.564, 43.958, 47.680
Angle α, β, γ (deg.)63.89, 80.03, 87.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein computationally designed four-helix bundle protein


Mass: 13266.452 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-41(b) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.92 Å3/Da / Density % sol: 36.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Mix 0.5 microliters of protein (20 mg/ml DRNN in 100 mM Ammonium Acetate) with 0.5 microliters of crystallization solution (0.2 M Magnesium Acetate, 20 % PEG 3350), pH 7, VAPOR DIFFUSION, ...Details: Mix 0.5 microliters of protein (20 mg/ml DRNN in 100 mM Ammonium Acetate) with 0.5 microliters of crystallization solution (0.2 M Magnesium Acetate, 20 % PEG 3350), pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97941 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 5, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 1.85→39.46 Å / Num. all: 16212 / Num. obs: 16212 / % possible obs: 96.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 25
Reflection shellResolution: 1.85→1.87 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 1.8 / Num. unique all: 391 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computationally-designed four helix bundle protein

Resolution: 1.854→39.458 Å / SU ML: 0.4 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 819 5.07 %RANDOM
Rwork0.176 ---
all0.1779 16156 --
obs0.1779 16156 96.28 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.141 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.3787 Å20.5973 Å2-5.6496 Å2
2---6.8948 Å25.2371 Å2
3----6.4839 Å2
Refinement stepCycle: LAST / Resolution: 1.854→39.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 0 140 1840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111758
X-RAY DIFFRACTIONf_angle_d1.0682363
X-RAY DIFFRACTIONf_dihedral_angle_d13.817707
X-RAY DIFFRACTIONf_chiral_restr0.057281
X-RAY DIFFRACTIONf_plane_restr0.005291
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8542-1.97040.31621260.2592489267793
1.9704-2.12250.25351600.20872540274896
2.1225-2.33610.22451390.17882552273697
2.3361-2.67410.2111260.17042617267897
2.6741-3.36880.22591450.15892588268598
3.3688-39.46730.18171230.16892551261296
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)
12.36251.9457-0.59435.1277-5.25127.0502-0.07180.03610.1418-0.04560.88861.5523-0.172-0.6474-0.6140.08490.01840.0120.2228-0.01710.30112.1942-26.7625-5.8843
23.3029-0.42321.14983.5516-4.97239.777-0.08680.0080.17570.49030.052-0.0159-0.24770.10430.06320.0965-0.0415-0.01110.2178-0.04940.193510.0344-16.9154-3.5148
34.53262.5167-2.12421.3945-1.01911.81260.2788-0.2464-0.34740.8359-0.5479-1.53510.04050.64620.26990.21030.0064-0.09350.36730.0030.384117.4516-21.5887-6.3042
43.96191.40382.07387.01611.45527.7572-0.04170.429-0.05180.08380.1218-0.65220.05540.811-0.03750.16760.05980.00980.4009-0.03840.231113.6773-20.7489-13.8288
54.6097-2.96452.25913.22-3.14816.913-0.2254-0.5366-0.18020.42970.95711.409-0.4055-1.0308-0.55320.18010.01180.06190.3518-0.01290.30296.3014-5.080414.225
63.4575-3.00122.62469.2778-3.94385.76240.0989-0.0582-0.2067-0.0446-0.01120.11270.3910.0455-0.0740.1396-0.02460.03410.2653-0.03070.204312.8201-15.48289.7854
75.2585-2.76640.77155.06410.51592.899-0.11940.35060.0831-0.96460.0532-0.70830.01790.69640.1290.1476-0.02320.06120.3364-0.01630.294320.0017-9.7817.7668
84.2612-0.61320.10623.88371.01157.9633-0.18980.02970.1015-0.40380.0362-0.56610.25460.65330.05980.1678-0.04210.01180.3158-0.00070.162819.8771-10.153116.5675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:31)
2X-RAY DIFFRACTION2chain 'A' and (resseq 32:56)
3X-RAY DIFFRACTION3chain 'A' and (resseq 57:76)
4X-RAY DIFFRACTION4chain 'A' and (resseq 77:105)
5X-RAY DIFFRACTION5chain 'B' and (resseq 4:29)
6X-RAY DIFFRACTION6chain 'B' and (resseq 30:56)
7X-RAY DIFFRACTION7chain 'B' and (resseq 57:76)
8X-RAY DIFFRACTION8chain 'B' and (resseq 77:105)

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