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Basic information

Entry
Database: PDB / ID: 4ndj
TitleCrystal Structure of a computational designed engrailed homeodomain variant fused with YFP
ComponentsGreen fluorescent protein, chimeric construct,GFP-like fluorescent chromoprotein FP506, related
Keywordsfluorescent protein / de novo protein / helix-turn-helix
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / GFP-like fluorescent chromoprotein FP506, related
Function and homology information
Biological speciesAequorea victoria (jellyfish)
Eimeria acervulina (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMou, Y. / Mayo, S.L.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Using Molecular Dynamics Simulations as an Aid in the Prediction of Domain Swapping of Computationally Designed Protein Variants.
Authors: Mou, Y. / Huang, P.S. / Thomas, L.M. / Mayo, S.L.
History
DepositionOct 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Other
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Aug 19, 2015Group: Database references
Revision 1.4Oct 18, 2017Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_distant_solvent_atoms / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _struct_ref_seq.db_align_beg ..._entity.pdbx_description / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein, chimeric construct,GFP-like fluorescent chromoprotein FP506, related


Theoretical massNumber of molelcules
Total (without water)34,5431
Polymers34,5431
Non-polymers00
Water5,999333
1
A: Green fluorescent protein, chimeric construct,GFP-like fluorescent chromoprotein FP506, related

A: Green fluorescent protein, chimeric construct,GFP-like fluorescent chromoprotein FP506, related


Theoretical massNumber of molelcules
Total (without water)69,0862
Polymers69,0862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x,y,-z-11
Buried area4730 Å2
ΔGint-15 kcal/mol
Surface area25260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.420, 104.420, 80.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-377-

HOH

21A-502-

HOH

31A-514-

HOH

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Components

#1: Protein Green fluorescent protein, chimeric construct,GFP-like fluorescent chromoprotein FP506, related


Mass: 34542.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Eimeria acervulina (eukaryote)
Gene: GFP, EAH_00062270 / Production host: Escherichia coli (E. coli) / References: UniProt: U6GSR1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTALLIZED SEQUENCE REPRESENTS A FUSED PROTEIN. THE N-TERMINAL SEQUENCE, WHICH IS ...THE CRYSTALLIZED SEQUENCE REPRESENTS A FUSED PROTEIN. THE N-TERMINAL SEQUENCE, WHICH IS COMPUTATIONALLY DESIGNED, IS BASED ON THE WILD-TYPE PROTEIN ENGRAILED HOMEODOMAIN (UNIPROT P02836). THE COMPUTATIONAL DESIGN PROCESS IS PURELY PHYSICAL-BASED WITHOUT USING ANY DATABASE ALIGNMENTS

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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: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.8 M monosodium phosphate, 1.2 M dipotassium phosphate, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionHighest resolution: 1.85 Å / Num. obs: 39983

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Processing

Software
NameVersionClassification
BlueIcedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→28.961 Å / SU ML: 0.16 / σ(F): 1.38 / Phase error: 17.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1999 1891 4.97 %
Rwork0.1731 --
obs0.1745 38078 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→28.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2294 0 0 333 2627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072347
X-RAY DIFFRACTIONf_angle_d1.1913167
X-RAY DIFFRACTIONf_dihedral_angle_d16.561884
X-RAY DIFFRACTIONf_chiral_restr0.08331
X-RAY DIFFRACTIONf_plane_restr0.005412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89630.22961150.19222577X-RAY DIFFRACTION100
1.8963-1.94760.20291440.17032542X-RAY DIFFRACTION100
1.9476-2.00490.18221340.16072570X-RAY DIFFRACTION100
2.0049-2.06960.19491430.16632558X-RAY DIFFRACTION100
2.0696-2.14350.18471100.16762587X-RAY DIFFRACTION100
2.1435-2.22930.21581310.17412602X-RAY DIFFRACTION100
2.2293-2.33070.20911410.17322547X-RAY DIFFRACTION100
2.3307-2.45350.24031290.17962600X-RAY DIFFRACTION100
2.4535-2.60720.20291470.18012578X-RAY DIFFRACTION100
2.6072-2.80830.21341440.17872609X-RAY DIFFRACTION100
2.8083-3.09060.21811500.18052603X-RAY DIFFRACTION100
3.0906-3.53720.1751380.16892635X-RAY DIFFRACTION100
3.5372-4.45390.18451410.15392641X-RAY DIFFRACTION99
4.4539-28.96440.2041240.19072538X-RAY DIFFRACTION90
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)
14.0906-0.14370.51613.3086-0.29411.31660.09950.3668-0.3599-0.41150.0439-0.48660.07730.1955-0.0920.20240.02030.00810.1322-0.03260.33515.2967.1238-43.7959
20.90420.50260.96561.86251.05794.71820.1727-0.03680.03260.16360.01180.5223-0.1425-0.17370.05250.2728-0.0218-0.05450.08810.00430.3516-10.321617.0803-36.3319
30.96640.30190.18531.46940.26320.91320.0162-0.1257-0.1880.1669-0.0275-0.13850.2080.02470.00470.32180.0136-0.01110.10460.0230.16647.369533.8042-17.7245
41.1554-0.09880.51261.3138-0.03040.7482-0.05520.08190.0492-0.0438-0.0054-0.1367-0.12860.17550.0130.2990.00780.01580.14380.00630.17719.733844.3445-23.7799
50.52270.02090.02721.43190.24610.65210.0467-0.002-0.06030.1077-0.0409-0.06270.03420.007-0.00730.31670.0004-0.00890.13030.00780.14993.495539.624-19.8655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:33 )A1 - 33
2X-RAY DIFFRACTION2( CHAIN A AND RESID 34:59 )A34 - 59
3X-RAY DIFFRACTION3( CHAIN A AND RESID 60:178 )A60 - 178
4X-RAY DIFFRACTION4( CHAIN A AND RESID 179:220 )A179 - 220
5X-RAY DIFFRACTION5( CHAIN A AND RESID 221:280 )A221 - 280

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