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Basic information

Entry
Database: PDB / ID: 4ndk
TitleCrystal structure of a computational designed engrailed homeodomain variant fused with YFP
ComponentsE23P-YFP, GFP-like fluorescent chromoprotein FP506, related, chimeric construct,
Keywordsfluorescent protein / de novo protein / helix-turn-helix
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
GFP-like fluorescent chromoprotein FP506, related
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Eimeria acervulina (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.1Jul 15, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Oct 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.db_code ..._entity.pdbx_description / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _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.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_name / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_ref_seq_dif.seq_num
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E23P-YFP, GFP-like fluorescent chromoprotein FP506, related, chimeric construct,
B: E23P-YFP, GFP-like fluorescent chromoprotein FP506, related, chimeric construct,


Theoretical massNumber of molelcules
Total (without water)69,0222
Polymers69,0222
Non-polymers00
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-10 kcal/mol
Surface area24210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.890, 192.650, 107.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein E23P-YFP, GFP-like fluorescent chromoprotein FP506, related, chimeric construct,


Mass: 34510.871 Da / Num. of mol.: 2
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.: 398 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium chloride, 12% v/v 2-propanol, 0.1 M sodium acetate, pH 4.6, 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: Dec 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→34 Å / Num. obs: 35208

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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: 2.3→34 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 1756 4.99 %
Rwork0.1901 --
obs0.1929 35178 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4454 0 0 398 4852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074558
X-RAY DIFFRACTIONf_angle_d1.1556149
X-RAY DIFFRACTIONf_dihedral_angle_d16.5961723
X-RAY DIFFRACTIONf_chiral_restr0.068642
X-RAY DIFFRACTIONf_plane_restr0.005801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36220.36231430.2732522X-RAY DIFFRACTION100
2.3622-2.43170.30361330.24652525X-RAY DIFFRACTION100
2.4317-2.51020.28381350.22042559X-RAY DIFFRACTION100
2.5102-2.59990.25531330.2172559X-RAY DIFFRACTION100
2.5999-2.70390.29671430.22192567X-RAY DIFFRACTION100
2.7039-2.82690.27411420.21692558X-RAY DIFFRACTION100
2.8269-2.97590.30661200.21992568X-RAY DIFFRACTION100
2.9759-3.16220.27331520.21272565X-RAY DIFFRACTION100
3.1622-3.40620.27771200.20222590X-RAY DIFFRACTION100
3.4062-3.74860.26971590.19282554X-RAY DIFFRACTION99
3.7486-4.29010.17771250.16032597X-RAY DIFFRACTION99
4.2901-5.40170.18471320.14062603X-RAY DIFFRACTION98
5.4017-34.35950.22811190.18122655X-RAY DIFFRACTION96
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)
10.0009-0.00050.0022-0.00060.00080.00590.0540.00980.02680.03340.0387-0.00740.014-0.0313-0.00030.6496-0.01540.08640.2695-0.00690.253217.483998.396683.1962
20.0374-0.0123-0.02030.00620.00520.0143-0.0280.01570.00260.07560.017-0.05430.00890.0418-0.01070.7207-0.1737-0.33270.36480.1640.19627.51998.174679.7395
30.0368-0.0319-0.04190.32730.24430.1854-0.1516-0.00420.02460.1306-0.1559-0.1052-0.04460.0876-0.09280.7042-0.1478-0.03560.25690.06560.200318.689686.295380.7803
40.0180.0433-0.01260.12420.01750.0179-0.0132-0.0163-0.0319-0.08250.0355-0.0207-0.0375-0.0078-0.03370.0433-0.14430.26690.0990.1394-0.05618.101560.714759.4078
50.09320.1028-0.01240.1491-0.02920.0098-0.03260.0274-0.21720.1494-0.0758-0.1369-0.13720.1136-0.02420.1328-0.21770.08680.33390.07730.138316.737867.111470.5885
60.01820.0031-0.02130.01760.01470.0396-0.0169-0.0046-0.0885-0.01470.0427-0.0178-0.05990.00490.02290.1758-0.1290.10950.26860.03820.163417.242267.073359.1093
70.10630.11820.01980.29040.10970.0770.1099-0.1152-0.1831-0.14180.1128-0.1852-0.13050.00040.2760.067-0.11080.12720.12790.0740.26115.076853.71458.8032
80.00480.0042-0.00190.004-00.0179-0.0162-0.03650.01930.02850.0365-0.06270.0463-0.0059-0.00290.2443-0.1455-0.13410.43910.03530.303524.240765.516574.2331
90.1276-0.0235-0.07320.01950.06630.31450.1866-0.1459-0.1656-0.00830.1258-0.04090.02290.10610.34290.0796-0.1977-0.11430.32670.19920.564120.959655.007368.2382
100.00650.0140.00110.04360.01430.0025-0.0097-0.0246-0.00150.07630.0105-0.0239-0.08690.0130.00950.2448-0.1763-0.01460.20370.09670.166315.985367.063173.8246
110.03780.0249-0.03040.0593-0.02850.0250.0366-0.00180.02030.0546-0.00230.0425-0.0032-0.08380.04860.0398-0.0718-0.00040.34830.05520.09192.413256.310463.801
120.01110.0044-0.00760.0085-0.00480.00460.0514-0.0324-0.0181-0.0952-0.03880.0854-0.1078-0.02450.00010.5167-0.063-0.01890.23530.0380.30556.066888.560266.0793
130.0855-0.0687-0.03560.06480.02610.01780.0998-0.0539-0.0637-0.05860.07720.22510.0024-0.07270.04830.4732-0.1027-0.04080.19590.08330.215511.5536101.185766.8851
140.0103-0.0410.03220.2045-0.09360.1136-0.0086-0.1013-0.04420.2871-0.2294-0.5084-0.01210.1204-0.64150.3479-0.0309-0.45620.13960.17940.367441.081118.758170.0245
150.236-0.17140.14350.85960.19620.28650.166-0.1293-0.10050.113-0.0216-0.63880.1088-0.00830.31280.02510.0418-0.09420.02760.05660.129435.5763116.244962.2408
160.019-0.00090.0050.0005-0.00050.00480.01390.0292-0.0487-0.0154-0.0225-0.00640.0332-0.01-0.02650.21270.0768-0.15030.22140.00540.148424.8655113.44754.8369
170.0935-0.00450.02960.1585-0.00650.0547-0.01240.06710.0117-0.0095-0.0007-0.00610.0103-0.02010.00240.15530.027-0.07580.1537-0.0380.111531.5657120.172254.9235
180.1395-0.0251-0.04220.13160.18090.31740.0422-0.0019-0.088-0.10720.0246-0.0014-0.0188-0.06060.19590.1813-0.0115-0.07090.13040.01410.101730.2576118.616959.2274
190.1474-0.0723-0.00480.15850.14690.1639-0.0673-0.02830.05010.1636-0.1822-0.1093-0.20260.1267-0.3630.3545-0.1489-0.37780.17460.06450.309137.0748125.709672.521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 8:18 )A8 - 18
2X-RAY DIFFRACTION2( CHAIN A AND RESID 19:37 )A19 - 37
3X-RAY DIFFRACTION3( CHAIN A AND RESID 38:60 )A38 - 60
4X-RAY DIFFRACTION4( CHAIN A AND RESID 61:117 )A61 - 117
5X-RAY DIFFRACTION5( CHAIN A AND RESID 121:157 )A121 - 157
6X-RAY DIFFRACTION6( CHAIN A AND RESID 158:168 )A158 - 168
7X-RAY DIFFRACTION7( CHAIN A AND RESID 169:200 )A169 - 200
8X-RAY DIFFRACTION8( CHAIN A AND RESID 201:211 )A201 - 211
9X-RAY DIFFRACTION9( CHAIN A AND RESID 212:240 )A212 - 240
10X-RAY DIFFRACTION10( CHAIN A AND RESID 241:261 )A241 - 261
11X-RAY DIFFRACTION11( CHAIN A AND RESID 262:281 )A262 - 281
12X-RAY DIFFRACTION12( CHAIN B AND RESID 8:37 )B8 - 37
13X-RAY DIFFRACTION13( CHAIN B AND RESID 38:61 )B38 - 61
14X-RAY DIFFRACTION14( CHAIN B AND RESID 62:117 )B62 - 117
15X-RAY DIFFRACTION15( CHAIN B AND RESID 121:200 )B121 - 200
16X-RAY DIFFRACTION16( CHAIN B AND RESID 201:211 )B201 - 211
17X-RAY DIFFRACTION17( CHAIN B AND RESID 212:223 )B212 - 223
18X-RAY DIFFRACTION18( CHAIN B AND RESID 224:261 )B224 - 261
19X-RAY DIFFRACTION19( CHAIN B AND RESID 262:282 )B262 - 282

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