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- PDB-3k2a: Crystal structure of the homeobox domain of human homeobox protei... -

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Basic information

Entry
Database: PDB / ID: 3k2a
TitleCrystal structure of the homeobox domain of human homeobox protein Meis2
ComponentsHomeobox protein Meis2
KeywordsDNA BINDING PROTEIN / homeobox domain / human homeobox protein MEIS2 / DNA-binding / transcription / Homeobox / Nucleus / Phosphoprotein
Function / homology
Function and homology information


positive regulation of cardiac muscle myoblast proliferation / negative regulation of myeloid cell differentiation / eye development / embryonic pattern specification / response to growth factor / pancreas development / transcription factor binding / response to mechanical stimulus / positive regulation of mitotic cell cycle / animal organ morphogenesis ...positive regulation of cardiac muscle myoblast proliferation / negative regulation of myeloid cell differentiation / eye development / embryonic pattern specification / response to growth factor / pancreas development / transcription factor binding / response to mechanical stimulus / positive regulation of mitotic cell cycle / animal organ morphogenesis / brain development / visual learning / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of cell population proliferation / chromatin / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Homeobox protein PKNOX/Meis, N-terminal / TALE/MEIS homeobox family N-terminal domain / : / Homeobox KN domain / Homeobox KN domain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily ...Homeobox protein PKNOX/Meis, N-terminal / TALE/MEIS homeobox family N-terminal domain / : / Homeobox KN domain / Homeobox KN domain / '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
ACETATE ION / Homeobox protein Meis2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsLam, R. / Soloveychik, M. / Battaile, K.P. / Romanov, V. / Lam, K. / Beletskaya, I. / Gordon, E. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: To be Published
Title: Crystal structure of the homeobox domain of human homeobox protein Meis2
Authors: Lam, R. / Soloveychik, M. / Battaile, K.P. / Romanov, V. / Lam, K. / Beletskaya, I. / Gordon, E. / Pai, E.F. / Chirgadze, N.Y.
History
DepositionSep 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 27, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 Meis2
B: Homeobox protein Meis2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9486
Polymers15,7592
Non-polymers1894
Water86548
1
A: Homeobox protein Meis2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9743
Polymers7,8801
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Homeobox protein Meis2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9743
Polymers7,8801
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Homeobox protein Meis2
B: Homeobox protein Meis2
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)127,58748
Polymers126,07516
Non-polymers1,51232
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area33190 Å2
ΔGint-260 kcal/mol
Surface area39020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.597, 113.597, 50.251
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-500-

CL

21B-500-

CL

31A-37-

HOH

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Components

#1: Protein Homeobox protein Meis2 / Meis1-related protein 1


Mass: 7879.710 Da / Num. of mol.: 2 / Fragment: Residues 281-345 (homeobox domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEIS2, MRG1 / Plasmid: pET28-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14770
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% PEG4000, 8% isopropanol, 0.1M sodium acetate, 10mM L-proline, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 5, 2009 / Details: Si(111) double-crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 12319 / % possible obs: 99.6 % / Redundancy: 28.5 % / Rmerge(I) obs: 0.063 / Χ2: 1.667 / Net I/σ(I): 17.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-2.02290.47312120.957100
2.02-2.128.90.3412111.236100
2.1-2.229.10.20412141.127100
2.2-2.3128.70.16512151.451100
2.31-2.4629.10.10812141.438100
2.46-2.6528.80.08512381.553100
2.65-2.9128.90.07112271.757100
2.91-3.3328.60.05812351.84499.9
3.33-4.228.20.04712641.78299.9
4.2-5025.80.04712893.63196.5

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1001.9524.16105741616
ANO_10.42301.9524.16105670
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_18.23-24.160010155
ISO_15.99-8.230020083
ISO_14.94-5.990026881
ISO_14.3-4.940032581
ISO_13.86-4.30036283
ISO_13.53-3.860041281
ISO_13.28-3.530044984
ISO_13.07-3.280048079
ISO_12.9-3.070051085
ISO_12.75-2.90054585
ISO_12.62-2.750057776
ISO_12.51-2.620061277
ISO_12.41-2.510062489
ISO_12.33-2.410065781
ISO_12.25-2.330068683
ISO_12.18-2.250070482
ISO_12.11-2.180073276
ISO_12.05-2.110076092
ISO_12-2.050076582
ISO_11.95-20080581
ANO_18.23-24.160.4450960
ANO_15.99-8.230.24601990
ANO_14.94-5.990.25702680
ANO_14.3-4.940.28603250
ANO_13.86-4.30.32903620
ANO_13.53-3.860.3204120
ANO_13.28-3.530.304490
ANO_13.07-3.280.31904800
ANO_12.9-3.070.33305100
ANO_12.75-2.90.33205450
ANO_12.62-2.750.35105770
ANO_12.51-2.620.4206120
ANO_12.41-2.510.4706240
ANO_12.33-2.410.50906570
ANO_12.25-2.330.56806860
ANO_12.18-2.250.64207040
ANO_12.11-2.180.69107320
ANO_12.05-2.110.76707600
ANO_12-2.050.84607640
ANO_11.95-20.88608050
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 12190
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.72-10062.20.809505
4.56-5.7256.50.912503
3.97-4.56560.933510
3.59-3.9755.50.925509
3.33-3.5961.10.908506
3.13-3.3359.20.914504
2.97-3.1356.30.893501
2.84-2.9755.80.901506
2.73-2.8459.10.884503
2.63-2.73550.895505
2.55-2.6353.60.884515
2.47-2.5558.10.895511
2.4-2.4760.20.883510
2.34-2.455.70.879513
2.29-2.3455.40.876512
2.24-2.2963.20.876537
2.19-2.2462.30.873536
2.14-2.1961.10.876560
2.1-2.1464.90.843559
2.06-2.167.70.866585
2.02-2.0667.30.79585
1.99-2.0273.30.778596
1.95-1.9971.80.708619

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.005data extraction
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→25.13 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.22 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.039 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.239 590 4.8 %RANDOM
Rwork0.215 ---
obs0.216 12250 99.17 %-
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 max: 61.75 Å2 / Biso mean: 29.967 Å2 / Biso min: 20.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.95→25.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 10 48 989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022962
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.9241303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2385109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.8523.67349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54915169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.084158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021731
X-RAY DIFFRACTIONr_mcbond_it0.7761.5565
X-RAY DIFFRACTIONr_mcangle_it1.4732917
X-RAY DIFFRACTIONr_scbond_it2.0553397
X-RAY DIFFRACTIONr_scangle_it3.3374.5386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.947-1.9970.317510.24584389599.888
1.997-2.0520.296470.24781586899.309
2.052-2.1110.233370.247808845100
2.111-2.1750.242350.24778181799.878
2.175-2.2460.271360.2275379399.496
2.246-2.3240.235590.21970677498.837
2.324-2.4110.275240.19872575199.734
2.411-2.5090.289300.22868272198.752
2.509-2.6190.169340.23566470199.572
2.619-2.7450.292350.22162165799.848
2.745-2.8920.22330.23959863898.903
2.892-3.0650.355220.22157560099.5
3.065-3.2730.171270.21953456898.768
3.273-3.530.247250.21151354199.445
3.53-3.860.218170.18647649599.596
3.86-4.3030.194180.18942744999.109
4.303-4.9440.242240.174387411100
4.944-5.9970.21140.22833735299.716
5.997-8.250.24130.24127228898.958
8.25-25.1250.25190.22814318980.423
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)
11.831-0.38-0.1383.08431.05622.21030.0457-0.03040.0023-0.24150.0309-0.011-0.24250.1187-0.07650.0879-0.05640.01620.0485-0.02880.056734.12139.97114.998
21.2856-0.5094-0.04916.07761.25541.112-0.077-0.00780.00580.3120.0490.20930.0121-0.06710.02810.1172-0.01980.05520.0212-0.02250.056328.6852.7235.476
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A284 - 338
2X-RAY DIFFRACTION2B283 - 338

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