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- PDB-1p7j: Crystal structure of engrailed homeodomain mutant K52E -

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Basic information

Entry
Database: PDB / ID: 1p7j
TitleCrystal structure of engrailed homeodomain mutant K52E
ComponentsSegmentation polarity homeobox protein engrailed
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation ...posterior compartment specification / analia development / anterior head segmentation / posterior head segmentation / anterior/posterior lineage restriction, imaginal disc / trunk segmentation / genital disc development / genital disc anterior/posterior pattern formation / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation / wing disc morphogenesis / neuroblast fate determination / imaginal disc-derived wing vein specification / segment polarity determination / ventral midline development / compartment pattern specification / gonad development / axon guidance / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of gene expression / sequence-specific DNA binding / negative regulation of neuron apoptotic process / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Homeobox domain engrailed / Homeobox engrailed, C-terminal / Homeobox engrailed-type, conserved site / Engrailed homeobox C-terminal signature domain / 'Homeobox' engrailed-type protein signature. / : / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. ...Homeobox domain engrailed / Homeobox engrailed, C-terminal / Homeobox engrailed-type, conserved site / Engrailed homeobox C-terminal signature domain / 'Homeobox' engrailed-type protein signature. / : / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Segmentation polarity homeobox protein engrailed
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStollar, E.J. / Mayor, U. / Lovell, S.C. / Federici, L. / Freund, S.M. / Fersht, A.R. / Luisi, B.F.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Crystal Structures of Engrailed Homeodomain Mutants: IMPLICATIONS FOR STABILITY AND DYNAMICS
Authors: Stollar, E.J. / Mayor, U. / Lovell, S.C. / Federici, L. / Freund, S.M. / Fersht, A.R. / Luisi, B.F.
#1: Journal: Protein Sci. / Year: 1994
Title: Structural studies of the engrailed homeodomain
Authors: Clarke, N.D. / Kissinger, C.R. / Desjarlais, J. / Gilliland, G.L. / Pabo, C.O.
#2: Journal: J.Mol.Biol. / Year: 1998
Title: Engrailed Homeodomain-DNA Complex at 2.2 A Resolution: A Detailed View of the Interface and Comparison with other Engrailed Structures
Authors: Fraenkel, E. / Rould, M.A. / Chambers, K.A. / Pabo, C.O.
History
DepositionMay 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Segmentation polarity homeobox protein engrailed
B: Segmentation polarity homeobox protein engrailed
C: Segmentation polarity homeobox protein engrailed
D: Segmentation polarity homeobox protein engrailed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1005
Polymers28,8934
Non-polymers2071
Water3,027168
1
A: Segmentation polarity homeobox protein engrailed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4302
Polymers7,2231
Non-polymers2071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Segmentation polarity homeobox protein engrailed


Theoretical massNumber of molelcules
Total (without water)7,2231
Polymers7,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Segmentation polarity homeobox protein engrailed


Theoretical massNumber of molelcules
Total (without water)7,2231
Polymers7,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Segmentation polarity homeobox protein engrailed


Theoretical massNumber of molelcules
Total (without water)7,2231
Polymers7,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.850, 51.679, 112.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Segmentation polarity homeobox protein engrailed


Mass: 7223.201 Da / Num. of mol.: 4 / Fragment: Homeodomain / Mutation: K52E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: EN / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P02836
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 30% PEG 3000, 100mM 2-(cyclohexylamino)ethanesulfonic acid (CHES), pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 mg/mlprotein1drop
230 %(w/v)PEG30001reservoir
3100 mMCHES1reservoirpH9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9779 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.1→19.24 Å / Num. obs: 15614 / Redundancy: 10.1 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 22
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 6.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 14837 / % possible obs: 98.3 % / Num. measured all: 159036
Reflection shell
*PLUS
% possible obs: 90.4 % / Rmerge(I) obs: 0.176

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ENH

1enh


Resolution: 2.1→19.25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.624 / SU ML: 0.181 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24126 777 5 %RANDOM
Rwork0.19814 ---
obs0.20026 14837 98.28 %-
all-15676 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.292 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 13 168 1913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211766
X-RAY DIFFRACTIONr_bond_other_d0.0010.021612
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.9382356
X-RAY DIFFRACTIONr_angle_other_deg0.63833727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9343205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.58715338
X-RAY DIFFRACTIONr_chiral_restr0.070.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021969
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02405
X-RAY DIFFRACTIONr_nbd_refined0.2350.3434
X-RAY DIFFRACTIONr_nbd_other0.1880.31535
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.5118
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0880.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.324
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.370
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.517
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.52551040
X-RAY DIFFRACTIONr_mcangle_it3.88261632
X-RAY DIFFRACTIONr_scbond_it3.9686726
X-RAY DIFFRACTIONr_scangle_it5.8457.5724
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.255 57
Rwork0.212 975
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)
1-108.871428.078395.6532134.9911-240.6898337.51464.4279-0.43353.5591-6.48290.67235.225611.72518.8906-5.10020.65710.5201-0.06031.0584-0.12590.990842.100235.139147.7928
23.722-0.0226-0.12721.2879-0.1030.3881-0.03140.1005-0.0137-0.08630.0072-0.02260.0485-0.01380.02420.16670.00360.00330.11730.02010.108630.933438.672356.2396
31.89418.715-1.6261-4.156210.455910.72390.27360.4758-1.3416-0.02390.21250.23980.18560.3935-0.48610.21710.02680.0120.1179-0.07070.206927.004530.459849.1633
41.9841-0.44660.98331.0588-1.23894.2287-0.0254-0.08750.01010.062-0.0718-0.0102-0.05060.04020.09720.16650.00350.00710.12020.02320.114335.3979.520918.7995
5-1.6975-3.4241-0.5295-4.24041.408117.79340.0170.01370.1857-0.7701-0.2177-0.19110.4651-0.65630.20070.2556-0.0451-0.00240.07750.02720.097435.92520.431325.6655
64.7476-0.360.14781.0464-0.0192.4933-0.05330.13310.13420.05930.01950.05420.0394-0.06950.03380.1235-0.0194-0.02050.1363-0.0940.15462.896531.998816.4648
72.87335.217317.69879.479-21.170735.8324-0.42671.31560.4643-1.37640.5280.4787-0.96560.6594-0.10130.164-0.0705-0.06910.18640.08960.0651-2.669838.89636.9013
8-574.3385-222.0714-125.078573.9752317.4766-487.7653.564712.0848-1.4978-0.27952.87212.76020.8190.8872-6.43690.27620.2170.05010.66760.00370.24949.68962.353431.6516
96.03811.4138-1.80611.0095-0.38912.0695-0.05630.19940.407-0.03360.10750.08250.0032-0.1124-0.05120.1092-0.0015-0.00830.11090.11230.179219.51755.356239.5879
1019.6329-5.0817-14.39553.41447.144416.6411-0.47371.39420.04840.1169-0.606-0.4105-0.1154-1.16871.07970.1768-0.1346-0.01550.13510.0670.094825.0597-1.634629.3803
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 63 - 6
2X-RAY DIFFRACTION2AA7 - 517 - 51
3X-RAY DIFFRACTION3AA52 - 5552 - 55
4X-RAY DIFFRACTION4BB7 - 517 - 51
5X-RAY DIFFRACTION5BB52 - 5552 - 55
6X-RAY DIFFRACTION6CC6 - 516 - 51
7X-RAY DIFFRACTION7CC52 - 5752 - 57
8X-RAY DIFFRACTION8DD1 - 61 - 6
9X-RAY DIFFRACTION9DD7 - 517 - 51
10X-RAY DIFFRACTION10DD52 - 5852 - 58
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.006
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg0.93

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