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- PDB-1p7i: CRYSTAL STRUCTURE OF ENGRAILED HOMEODOMAIN MUTANT K52A -

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Basic information

Entry
Database: PDB / ID: 1p7i
TitleCRYSTAL STRUCTURE OF ENGRAILED HOMEODOMAIN MUTANT K52A
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 / neuron differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of gene expression / negative regulation of neuron apoptotic process / sequence-specific DNA binding / 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)28,8685
Polymers28,6614
Non-polymers2071
Water1,802100
1
A: Segmentation polarity homeobox protein engrailed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3722
Polymers7,1651
Non-polymers2071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Segmentation polarity homeobox protein engrailed


Theoretical massNumber of molelcules
Total (without water)7,1651
Polymers7,1651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Segmentation polarity homeobox protein engrailed


Theoretical massNumber of molelcules
Total (without water)7,1651
Polymers7,1651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Segmentation polarity homeobox protein engrailed


Theoretical massNumber of molelcules
Total (without water)7,1651
Polymers7,1651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.664, 51.176, 108.253
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: 7165.165 Da / Num. of mol.: 4 / Fragment: Homeodomain / Mutation: K52A
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.: 100 / 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: 2.16 Å3/Da / Density % sol: 43 %
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: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→19.48 Å / Num. obs: 14829 / Redundancy: 4 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 4.8
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 14092 / % possible obs: 98.3 % / Num. measured all: 59319
Reflection shell
*PLUS
% possible obs: 91 %

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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→54.23 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.03 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The density at LEU 26 Chain C indicates a mixture of 2 rotamers, only one of which is modelled and accounts for the angular deviation.
RfactorNum. reflection% reflectionSelection details
Rfree0.23963 737 5 %RANDOM
Rwork0.1997 ---
obs0.20156 14092 98.3 %-
all-14862 --
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: 16.742 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 13 100 1834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211760
X-RAY DIFFRACTIONr_bond_other_d0.0010.021607
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9382355
X-RAY DIFFRACTIONr_angle_other_deg0.68633710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1683205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.53615329
X-RAY DIFFRACTIONr_chiral_restr0.0810.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021971
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02403
X-RAY DIFFRACTIONr_nbd_refined0.230.3397
X-RAY DIFFRACTIONr_nbd_other0.1870.31453
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3010.581
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2030.369
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2850.512
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0560.52
X-RAY DIFFRACTIONr_mcbond_it2.45251045
X-RAY DIFFRACTIONr_mcangle_it3.84461645
X-RAY DIFFRACTIONr_scbond_it3.7716715
X-RAY DIFFRACTIONr_scangle_it5.8257.5710
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
Rfree0.246 66
Rwork0.191 932
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)
130.7878-25.9743-20.988949.214241.5548127.3441.88472.9483-2.0068-1.2333-1.17580.8662-1.5843-0.7006-0.70890.10820.1386-0.14890.3006-0.11990.24593.858515.350545.5271
23.8265-0.0681-0.52330.8387-0.60311.281-0.05080.0769-0.082-0.02960.0044-0.0178-0.0212-0.03890.04630.21220.00540.00530.1785-0.03030.185414.532512.730754.0908
322.574-3.8362-0.948226.2864-8.926911.37660.07490.76781.54430.5277-0.1264-0.4888-0.1581-0.33750.05140.1859-0.0250.00210.22270.08940.221518.751320.40346.2335
41.7645-0.4128-0.97810.81451.21073.35530.0550.00680.05260.1454-0.0284-0.0318-0.03230.0077-0.02660.22420.0066-0.00330.15160.01090.19819.582441.506918.6557
510.053410.11991.377316.5581-0.238226.6430.04050.09840.7909-1.1685-0.26280.2667-1.15590.79050.22240.3044-0.0070.06240.1041-0.00930.22938.412550.41726.6306
67.9309-1.13530.11.49540.38562.3487-0.0602-0.60630.14410.00420.1278-0.05850.01640.0674-0.06760.17720.0137-0.01190.19480.02890.163219.36178.132293.7679
731.3549-11.981214.584216.525643.9305-10.17540.6232-3.23431.23991.42210.0838-0.8430.56520.1955-0.7070.25150.0239-0.09660.3248-0.22110.230823.401716.0059102.0087
8-1.39980.67453.2227.6498-5.00849.866-0.2311-0.5205-0.25210.22090.315-0.17820.2963-0.0681-0.08390.1702-0.0568-0.05290.09540.02060.29535.3489-1.64888.6873
99.1786-0.30171.30230.76630.43891.8884-0.2471-0.62510.469-0.07690.15080.0428-0.0107-0.20550.09620.17280.0084-0.00750.22080.02670.183741.75247.920593.8569
1011.2653-4.952715.5012.424312.643721.8430.24690.5653-0.65310.06890.0242-0.4270.04360.9832-0.27110.2071-0.05820.08670.167-0.01840.252947.1026-0.073185.5842
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 DIFFRACTION6CC7 - 517 - 51
7X-RAY DIFFRACTION7CC52 - 5552 - 55
8X-RAY DIFFRACTION8DD1 - 61 - 6
9X-RAY DIFFRACTION9DD7 - 517 - 51
10X-RAY DIFFRACTION10DD52 - 5652 - 56
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.29

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