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- PDB-4rdu: Crystal structure of a distal-less homeobox protein 5 (Dlx5) from... -

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Basic information

Entry
Database: PDB / ID: 4rdu
TitleCrystal structure of a distal-less homeobox protein 5 (Dlx5) from Homo sapiens at 1.85 A resolution
Components
  • (DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG)
  • Homeobox protein DLX-5
KeywordsTRANSCRIPTION/DNA / PF00046 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / TRANSCRIPTION / TRANSCRIPTION-DNA complex / Partnership for Stem Cell Biology / STEMCELL
Function / homology
Function and homology information


interneuron axon guidance / olfactory pit development / HMG box domain binding / anatomical structure formation involved in morphogenesis / olfactory bulb interneuron differentiation / endochondral ossification / embryonic limb morphogenesis / face morphogenesis / inner ear morphogenesis / roof of mouth development ...interneuron axon guidance / olfactory pit development / HMG box domain binding / anatomical structure formation involved in morphogenesis / olfactory bulb interneuron differentiation / endochondral ossification / embryonic limb morphogenesis / face morphogenesis / inner ear morphogenesis / roof of mouth development / BMP signaling pathway / epithelial cell differentiation / skeletal system development / positive regulation of epithelial cell proliferation / osteoblast differentiation / positive regulation of canonical Wnt signaling pathway / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / cell population proliferation / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Distal-less-like homeobox protein, N-terminal domain / Homeobox protein distal-less-like N terminal / Helix-turn-helix motif / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain ...Distal-less-like homeobox protein, N-terminal domain / Homeobox protein distal-less-like N terminal / 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
DNA / DNA (> 10) / Homeobox protein DLX-5
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL)
CitationJournal: To be published
Title: Crystal structure of a distal-less homeobox protein 5 (Dlx5) from Homo sapiens at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL)
History
DepositionSep 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software / Item: _software.classification / _software.name
Revision 1.2Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homeobox protein DLX-5
B: (DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG)
C: (DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG)
D: Homeobox protein DLX-5
E: (DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG)
F: (DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG)


Theoretical massNumber of molelcules
Total (without water)32,4456
Polymers32,4456
Non-polymers00
Water4,197233
1
A: Homeobox protein DLX-5
B: (DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG)
C: (DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG)


Theoretical massNumber of molelcules
Total (without water)16,2233
Polymers16,2233
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-17 kcal/mol
Surface area8020 Å2
MethodPISA
2
D: Homeobox protein DLX-5
E: (DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG)
F: (DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG)


Theoretical massNumber of molelcules
Total (without water)16,2233
Polymers16,2233
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-16 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.182, 42.913, 56.104
Angle α, β, γ (deg.)84.130, 77.330, 67.130
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGASNASNAA138 - 1985 - 65
21ARGARGASNASNDD138 - 1985 - 65
12DCDCDGDGBB1 - 141 - 14
22DCDCDGDGEE1 - 141 - 14
13DCDCDCDCCC1 - 131 - 13
23DCDCDCDCFF1 - 131 - 13

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Homeobox protein DLX-5 /


Mass: 7663.090 Da / Num. of mol.: 2 / Fragment: DNA binding residues 137-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BC006226, DLX5 / Plasmid: pET28bGB1Tev / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56178
#2: DNA chain
(DC)(DG)(DA)(DC)(DT)(DA)(DA)(DT)(DT)(DA)(DG)(DT)(DC)(DG)


Mass: 4279.804 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (135-198) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (135-198) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. IN THE CONSTRUCT LYS 135 WAS MUTATED TO HIS AND LYS 136 WAS MUTATED TO MET.

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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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.08M sodium chloride, 45.00% 2-methyl-2,4-pentanediol, 0.012M spermine tetrahydrochloride, 0.1M sodium cacodylate pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 24, 2014
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→22.303 Å / Num. all: 23348 / Num. obs: 23348 / % possible obs: 95.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 33.646 Å2 / Rsym value: 0.046 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.91.90.2712.5331517230.27194.1
1.9-1.951.90.233317316550.2395
1.95-2.011.90.1843.5314516350.18495.1
2.01-2.071.90.1414.6304815900.14194.9
2.07-2.141.90.1145.8295415330.11495.2
2.14-2.211.90.0946.7282514680.09495.8
2.21-2.291.90.0935.6278914520.09395.7
2.29-2.391.90.0758.7272214220.07596.3
2.39-2.491.90.0678.5253013050.06795.6
2.49-2.621.90.0629.9246012800.06296
2.62-2.761.90.05510.4229611950.05596.4
2.76-2.931.90.05211.1225611720.05296.7
2.93-3.131.90.04214.2212310990.04296.6
3.13-3.381.90.0435.119129970.04396.9
3.38-3.71.90.047.618069340.0497.1
3.7-4.141.90.0318.216248430.0397.1
4.14-4.781.90.03813.314777630.03897.7
4.78-5.851.90.03813.311896160.03897.3
5.85-8.271.90.0510.99384860.0596.4
8.27-22.3031.80.04714.43221800.04766.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
SCALA3.3.20data scaling
REFMAC5.7.0029refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IG7

1ig7


Resolution: 1.85→22.303 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 6.492 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3.TLS GROUPS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3.TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD (MOTION DETERMINATION) SERVER. 4. WATERS WERE EXCLUDED FROM TLS ASSIGNMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 1188 5.1 %RANDOM
Rwork0.1829 ---
obs0.185 23315 95.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 158.2 Å2 / Biso mean: 47.0789 Å2 / Biso min: 20.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å21.68 Å20.94 Å2
2---3.44 Å2-1.41 Å2
3---3.53 Å2
Refinement stepCycle: LAST / Resolution: 1.85→22.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1008 1114 0 233 2355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0152313
X-RAY DIFFRACTIONr_bond_other_d0.0020.021732
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.5153352
X-RAY DIFFRACTIONr_angle_other_deg1.40934015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9555133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.42821.91547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3715224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0051513
X-RAY DIFFRACTIONr_chiral_restr0.10.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021830
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02527
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A916MEDIUM POSITIONAL0.370.5
1A916MEDIUM THERMAL5.212
2B443MEDIUM POSITIONAL0.380.5
2B443MEDIUM THERMAL11.362
3C410MEDIUM POSITIONAL0.350.5
3C410MEDIUM THERMAL6.412
LS refinement shellResolution: 1.85→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 85 -
Rwork0.307 1571 -
all-1656 -
obs--90.84 %
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)
12.2604-0.2119-0.3261.7535-0.15811.5004-0.0456-0.00010.11750.10130.0240.0004-0.14910.03560.02150.06610.0266-0.05650.2269-0.0080.06743.570918.686464.8952
21.410.4243-0.97986.7192-1.00383.1087-0.08930.07220.075-0.47590.07280.0460.0542-0.08890.01640.11090.0242-0.07390.3359-0.00320.115547.053118.319953.3141
32.43020.4885-0.02197.8271.28753.6764-0.08450.1058-0.105-0.30580.0446-0.4550.10330.17790.03990.08880.0292-0.02270.30080.02210.078248.62116.175352.5788
42.56540.18250.13242.82220.22732.76390.0777-0.0157-0.06530.2301-0.0356-0.06680.20590.0216-0.04210.12590.0372-0.06720.2034-0.00460.041345.08641.123976.8714
55.50242.94920.01548.72140.26553.08550.2491-0.1552-0.22220.7125-0.27640.13670.4237-0.25550.02730.2473-0.00430.0050.1712-0.01640.019840.10013.204288.1196
63.66470.5540.21115.0134-0.05153.24350.1789-0.32620.01160.7119-0.23780.51970.1669-0.28040.05890.2296-0.00460.00950.2456-0.03030.097438.48435.060889.0283
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A138 - 198
2X-RAY DIFFRACTION2B1 - 14
3X-RAY DIFFRACTION3C1 - 14
4X-RAY DIFFRACTION4D137 - 198
5X-RAY DIFFRACTION5E1 - 14
6X-RAY DIFFRACTION6F1 - 13

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