[English] 日本語
Yorodumi
- PDB-1p7i: CRYSTAL STRUCTURE OF ENGRAILED HOMEODOMAIN MUTANT K52A -

+
Open data


ID or keywords:

Loading...

-
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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 %

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more