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- PDB-3a02: Crystal structure of Aristaless homeodomain -

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Basic information

Entry
Database: PDB / ID: 3a02
TitleCrystal structure of Aristaless homeodomain
ComponentsHomeobox protein aristaless
KeywordsGENE REGULATION / HOMEODOMAIN / Developmental protein / DNA-binding / Homeobox / Nucleus
Function / homology
Function and homology information


elongation of arista core / leg disc development / antennal morphogenesis / imaginal disc-derived leg morphogenesis / chaeta development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein-containing complex / nucleus
Similarity search - Function
OAR domain / OAR motif / OAR domain profile. / Helix-turn-helix motif / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain ...OAR domain / OAR motif / OAR domain profile. / Helix-turn-helix motif / 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
: / Homeobox protein aristaless
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsMiyazono, K. / Nagata, K. / Saigo, K. / Kojima, T. / Tanokura, M.
CitationJournal: Embo J. / Year: 2010
Title: Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless
Authors: Miyazono, K. / Zhi, Y. / Takamura, Y. / Nagata, K. / Saigo, K. / Kojima, T. / Tanokura, M.
History
DepositionFeb 28, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homeobox protein aristaless
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4493
Polymers7,3011
Non-polymers1482
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.810, 45.810, 48.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-3-

HOH

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Components

#1: Protein Homeobox protein aristaless /


Mass: 7301.347 Da / Num. of mol.: 1 / Fragment: Homeobox, residues 91-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: al, CG3935 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06453
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 30% PEG 400, 0.1M Cadmium chloride, 0.1M Acetate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1→39.67 Å / Num. obs: 32230 / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 9.186 Å2 / Rmerge F obs: 0.057 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.087 / Net I/σ(I): 18.23 / Num. measured all: 327246
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1-1.030.2690.455.823071234423400.4899.8
1.03-1.050.2050.3457.223104233123310.36100
1.05-1.080.1610.2728.722458225822580.29100
1.08-1.120.1240.21210.622352221422140.22100
1.12-1.150.0960.16512.921392210521050.17100
1.15-1.20.0790.14514.420935205020500.15100
1.2-1.240.0740.13215.420641200420040.14100
1.24-1.290.0650.12316.719793191419140.13100
1.29-1.350.0510.1081919225184418440.11100
1.35-1.410.0450.0962118213174817480.1100
1.41-1.490.040.08523.117733169116910.09100
1.49-1.580.0350.07825.316876160416040.08100
1.58-1.690.0290.07127.515823149914990.07100
1.69-1.830.0260.06828.914774140414030.0799.9
1.83-20.0240.06430.513715130113010.07100
2-2.240.0240.0623212270118011800.06100
2.24-2.580.0240.06232.610557105210410.0799
2.58-3.160.0240.06431.682478928690.0797.4
3.16-4.470.0280.06328.142797175730.0779.9
4.470.0280.06626.217884192610.0762.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FJL

1fjl


Resolution: 1→13.23 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 0.357 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18436 1633 5.1 %RANDOM
Rwork0.17219 30595 --
obs0.17279 32228 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 64.85 Å2 / Biso mean: 10.254 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.1 Å20 Å2
2--0.19 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1→13.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms431 0 2 99 532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022444
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.92597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.39322.17423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1981583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.137155
X-RAY DIFFRACTIONr_chiral_restr0.1450.264
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02331
X-RAY DIFFRACTIONr_mcbond_it0.771.5254
X-RAY DIFFRACTIONr_mcangle_it1.5952411
X-RAY DIFFRACTIONr_scbond_it2.9413190
X-RAY DIFFRACTIONr_scangle_it3.9614.5186
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 125 -
Rwork0.194 2213 -
all-2338 -
obs--99.83 %
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)
19.12661.2876-1.04915.20731.522312.7429-0.4326-0.0940.5634-0.66830.30670.6483-0.2748-0.1840.1260.0957-0.0315-0.09310.02910.0290.108730.54324.6270.396
21.184-0.37971.0510.146-0.26441.23690.01860.0237-0.01160.0097-0.00080.00050.02620.0305-0.01780.0718-0.0305-0.00080.03520.00180.027832.21818.487-0.19
32.4728-1.787-0.75841.31590.31582.89-0.00250.0868-0.04270.0003-0.05480.02140.0552-0.03240.05740.0385-0.0184-0.00680.0307-0.00880.052630.14311.1230.07
40.3775-1.04770.59834.47310.62354.34920.1611-0.04780.0321-0.30750.066-0.26420.4257-0.1239-0.22710.15-0.07610.02290.0563-0.01930.033330.0466.5895.785
55.32233.00280.29964.77160.13120.24450.0086-0.0893-0.1366-0.0420.0076-0.16550.0889-0.0116-0.01610.0417-0.0151-0.00660.036-0.0110.034936.99611.87112.006
63.85492.8841-3.953610.2672-5.32164.7545-0.25010.15280.0287-0.17960.2268-0.21140.244-0.19230.02320.0335-0.02380.0090.0528-0.00640.03239.58417.8516.609
71.29980.7164-1.99770.7702-0.66733.84820.0160.05410.0434-0.01140.0363-0.0173-0.0662-0.1687-0.05230.0302-0.0112-0.00980.0572-0.00050.038134.47821.1959.899
81.87481.05621.19641.254-0.04171.5481-0.06920.07530.0038-0.00970.0544-0.0071-0.06290.02590.01480.0305-0.012-0.00630.0496-0.00050.033726.95416.0069.748
90.3791-0.6760.56391.2215-0.83683.19330.0244-0.0098-0.0234-0.03840.00030.04770.1452-0.1207-0.02470.0375-0.0243-0.00920.0544-0.00070.03320.1099.7485.867
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A91 - 95
2X-RAY DIFFRACTION2A96 - 100
3X-RAY DIFFRACTION3A101 - 105
4X-RAY DIFFRACTION4A106 - 110
5X-RAY DIFFRACTION5A111 - 116
6X-RAY DIFFRACTION6A117 - 121
7X-RAY DIFFRACTION7A122 - 127
8X-RAY DIFFRACTION8A128 - 135
9X-RAY DIFFRACTION9A136 - 141

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