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- PDB-5jlx: AntpHD with 15bp DNA duplex S-monothioated at Cytidine-8 -

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Basic information

Entry
Database: PDB / ID: 5jlx
TitleAntpHD with 15bp DNA duplex S-monothioated at Cytidine-8
Components
  • DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C7S)P*AP*TP*TP*AP*GP*AP*G)-3')
  • DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')
  • Homeotic protein antennapediaHomeosis
KeywordsTranscription Regulator/DNA / HOMEODOMAIN / DNA-BINDING PROTEIN / COMPLEX (HOMEODOMAIN-DNA) / TRANSCRIPTION-DNA COMPLEX / Transcription Regulator-DNA complex / monothiolated DNA
Function / homology
Function and homology information


specification of segmental identity, antennal segment / specification of segmental identity, thorax / neuroblast development / muscle cell fate specification / lymph gland development / ventral cord development / anterior/posterior axis specification / anterior/posterior pattern specification / midgut development / regulation of neurogenesis ...specification of segmental identity, antennal segment / specification of segmental identity, thorax / neuroblast development / muscle cell fate specification / lymph gland development / ventral cord development / anterior/posterior axis specification / anterior/posterior pattern specification / midgut development / regulation of neurogenesis / heart development / 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 transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
Homeobox protein, antennapedia type / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain ...Homeobox protein, antennapedia type / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / 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
NICKEL (II) ION / DNA / DNA (> 10) / Homeotic protein antennapedia
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.748 Å
AuthorsWhite, M.A. / Zandarashvili, L. / Iwahara, J. / Nguyen, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Chembiochem / Year: 2016
Title: Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein-DNA Affinity.
Authors: Nguyen, D. / Zandarashvili, L. / White, M.A. / Iwahara, J.
History
DepositionApr 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Structure summary
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Database references / Category: pdbx_audit_support / struct_ref_seq
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.5Sep 27, 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_conn_type
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homeotic protein antennapedia
B: DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C7S)P*AP*TP*TP*AP*GP*AP*G)-3')
C: DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')
D: Homeotic protein antennapedia
E: DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C7S)P*AP*TP*TP*AP*GP*AP*G)-3')
F: DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4859
Polymers34,3096
Non-polymers1763
Water52229
1
A: Homeotic protein antennapedia
B: DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C7S)P*AP*TP*TP*AP*GP*AP*G)-3')
C: DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2725
Polymers17,1543
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-23 kcal/mol
Surface area8670 Å2
MethodPISA
2
D: Homeotic protein antennapedia
E: DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C7S)P*AP*TP*TP*AP*GP*AP*G)-3')
F: DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2134
Polymers17,1543
Non-polymers591
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-26 kcal/mol
Surface area8780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.864, 75.581, 91.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11D-106-

HOH

DetailsThere are two protein:DNA complexes in the a.u.

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Components

#1: Protein Homeotic protein antennapedia / Homeosis


Mass: 7961.297 Da / Num. of mol.: 2 / Mutation: C335S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Antp, CG1028 / Production host: Escherichia coli (E. coli) / References: UniProt: P02833
#2: DNA chain DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C7S)P*AP*TP*TP*AP*GP*AP*G)-3')


Mass: 4667.128 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: DNA chain DNA (5'-D(*TP*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3')


Mass: 4525.944 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20mM bis-Tris propane, 10mM NiCl2, 4-6% 2-methyl-2,4-pentanediol
PH range: 6.0 - 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.748→50 Å / Num. obs: 11412 / % possible obs: 99.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.152 / Rsym value: 0.064 / Net I/σ(I): 4.4
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.302 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XID

4xid


Resolution: 2.748→36.666 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 455 5 %
Rwork0.1926 --
obs0.1954 9098 78.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.748→36.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 1218 3 29 2298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072434
X-RAY DIFFRACTIONf_angle_d0.7863526
X-RAY DIFFRACTIONf_dihedral_angle_d26.5391236
X-RAY DIFFRACTIONf_chiral_restr0.042377
X-RAY DIFFRACTIONf_plane_restr0.004241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.748-3.14550.37881030.27531960X-RAY DIFFRACTION55
3.1455-3.96220.2571550.19592950X-RAY DIFFRACTION82
3.9622-36.66960.22061970.17853733X-RAY DIFFRACTION99
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)
10.07930.1070.01560.2455-0.06790.1054-0.2524-0.2647-0.1306-0.0528-0.0616-0.43420.2151-0.0169-0.07710.34170.13610.03260.489-0.14870.323924.494814.23771.7546
20.03480.0373-0.0010.0424-0.010.0022-0.0126-0.0217-0.13760.00260.1135-0.023-0.0075-0.11280.01330.49050.2273-0.04780.4266-0.040.310117.183914.46567.5946
30.11710.02120.07170.00970.08020.3549-0.0739-0.04160.0048-0.11050.04330.21850.20010.082-0.1499-0.22950.5156-0.73530.04890.527-0.75039.478414.80438.1004
40.0242-0.0147-0.01020.0160.00590.0123-0.0580.08440.10020.2989-0.0775-0.0450.3282-0.1658-0.00010.7620.2024-0.29070.6677-0.15490.7985.704120.99372.4133
50.04830.0249-0.05030.0111-0.03230.0583-0.5358-0.1331-0.048-0.4036-0.40280.253-0.2264-0.1055-0.00250.34590.0777-0.05480.6623-0.11120.442512.34929.4024.3797
60.03090.00860.02020.02-0.00690.0140.1273-0.2344-0.02060.02450.055-0.0291-0.01670.0728-0.00120.4317-00.01330.5201-0.05940.502518.695826.19257.6725
70.10710.1141-0.01770.1297-0.01450.0055-0.21950.1762-0.1198-0.1736-0.0637-0.1885-0.2668-0.0204-0.04030.51980.1016-0.08060.4830.10690.28720.543624.40270.093
80.00710.0038-0.0216-0.00060.00040.0112-0.19160.39620.1119-0.3588-0.24610.14670.2752-0.13430.00040.22960.0268-0.0410.38540.02050.416414.405319.064-2.9278
90.1143-0.0102-0.03130.0095-0.00380.0051-0.02590.07530.0947-0.11010.0650.1420.1629-0.21390.15150.5179-0.0083-0.28780.5536-0.21310.72588.937112.4765-3.3529
100.0102-0.00270.00780.00660.00280.0074-0.23070.01590.00890.08120.03420.08910.0909-0.02470.00051.361-0.1807-0.01340.6906-0.08361.00383.78427.6896-3.0351
110.00490.02350.00480.3152-0.31840.30790.07540.13730.18340.0166-0.2479-0.1137-0.10440.2144-0.1170.82990.28-0.10450.6010.23310.76966.468334.6891-11.4677
120.56720.3722-0.53810.821-0.12740.53320.79340.5063-0.72850.0129-0.31280.28130.1217-0.18960.07910.82490.2632-0.290.7146-0.12030.659810.202215.5232-13.7931
130.00890.00030.00930.0214-0.00330.00540.13160.6109-0.4756-0.114-0.05890.2009-0.14830.14140.00050.70250.1824-0.11070.71690.02960.580327.23948.6331-10.0784
140.6457-0.2842-0.4040.61950.29620.23250.10710.571-0.44450.5922-0.3941-0.3873-0.1511-0.796-0.04060.75360.1452-0.18260.4579-0.10950.508621.58515.7992-8.6998
150.0075-0.02770.01230.1725-0.10970.0646-0.02030.67030.27770.1362-0.13570.0089-0.40980.07120.00531.05850.572-0.1821.09640.10360.794913.745221.4198-17.6801
160.03160.0377-0.01080.0342-0.0140.01360.33580.04840.0725-0.29660.00180.14160.0484-0.1770.00031.11110.1329-0.08550.5441-0.11320.71260.797127.7351-11.6482
170.00350.0086-0.00060.0008-0.0037-0.0001-0.37020.23150.20960.4746-0.2711-0.0447-0.2847-0.05490.00060.6148-0.0088-0.17340.45270.01630.584715.713630.820529.2569
180.01190.01570.01080.0193-0.00450.0134-0.42240.21210.0741-0.183-0.19740.1037-0.30620.13140.00070.36010.0876-0.00350.47820.02940.576112.709726.893117.4892
190.3147-0.0366-0.00070.0227-0.05470.21550.0389-0.1657-0.223-0.11060.2480.01750.0641-0.21730.1943-0.07670.132-0.44720.1597-0.06930.134211.917517.945218.5551
200.0385-0.0470.06270.0884-0.0740.1036-0.021-0.13290.0263-0.16010.02990.2980.0613-0.2783-0.03210.2952-0.10560.18670.2715-0.0740.577910.078511.057119.048
210.1257-0.02930.0510.017-0.00190.16760.1433-0.19420.0422-0.2164-0.03230.20450.01430.18640.03060.42870.25490.2180.16110.08540.541920.188910.265424.5741
220.0074-0.00090.00570.16120.01850.01520.05440.2895-0.0888-0.24880.08450.1843-0.02020.10860.09350.19890.01270.12550.4077-0.09040.338624.100914.07219.6314
230.0027-0.0013-0.00020.0180.00230.00930.06660.014-0.1396-0.02080.2774-0.4499-0.1957-0.0577-0.00150.2760.09390.00080.37080.08950.509623.001321.865219.0714
240.0209-0.02880.01680.0368-0.01820.01850.0978-0.0768-0.1588-0.0373-0.1125-0.0067-0.1417-0.06510.00410.5737-0.1450.0230.57490.08920.231423.853622.717224.7137
250.1683-0.0768-0.02970.0280.01490.0339-0.3281-0.4105-0.2236-0.1294-0.14760.22860.0922-0.0366-0.17390.29270.08650.03140.3310.04040.26615.666918.641828.8672
260.01570.00370.01390.00750.010.0107-0.15880.0475-0.21360.26140.134-0.143-0.0509-0.037-00.34720.02920.11050.66460.15730.59026.694613.889829.2731
270.01430.00840.00610.0032-0.00020.0069-0.04180.0424-0.0325-0.1541-0.05030.06690.0768-0.01170.00010.6043-0.18990.07350.945-0.07820.55970.724613.073829.8959
28-0.0032-0.00590.0375-0.0111-0.02880.0876-0.22320.61750.2760.41260.22460.247-0.3645-0.2014-0.00020.31370.0186-0.01770.50310.07970.514524.53997.777636.8248
290.267-0.13980.24870.3611-0.20870.2437-0.13280.37150.11550.462-0.230.28620.1625-0.2325-0.50820.65140.19440.37760.60290.18880.70959.133318.851942.0381
300.03140.0220.04650.01240.02130.02560.03040.21950.21360.46540.00580.1735-0.41420.49410.00010.68570.2468-0.25370.85010.02510.7828.912433.917735.7797
310.0039-0.0079-0.00970.01210.01210.0123-0.52270.18250.03650.3384-0.3967-0.03140.0303-0.21690.00210.59340.12340.07830.5613-0.21271.0158-1.200430.916935.8541
320.11770.0906-0.01660.1528-0.09120.1068-0.0422-0.03610.24680.604-0.25880.1596-0.15130.0768-0.00190.4510.1889-0.01240.6002-0.14460.625313.353924.860834.2385
331.137-0.4762-0.79040.9820.60780.7148-0.55420.2338-0.31880.54030.0877-0.4156-0.5182-0.3548-0.05820.97870.181-0.17120.69010.05030.740819.42778.64441.0414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:13)
2X-RAY DIFFRACTION2(chain A and resid 14:17)
3X-RAY DIFFRACTION3(chain A and resid 18:23)
4X-RAY DIFFRACTION4(chain A and resid 24:28)
5X-RAY DIFFRACTION5(chain A and resid 29:33)
6X-RAY DIFFRACTION6(chain A and resid 34:38)
7X-RAY DIFFRACTION7(chain A and resid 39:44)
8X-RAY DIFFRACTION8(chain A and resid 45:52)
9X-RAY DIFFRACTION9(chain A and resid 53:56)
10X-RAY DIFFRACTION10(chain A and resid 57:61)
11X-RAY DIFFRACTION11(chain B and resid 1:5)
12X-RAY DIFFRACTION12(chain B and resid 6:11)
13X-RAY DIFFRACTION13(chain B and resid 12:15)
14X-RAY DIFFRACTION14(chain C and resid 1:7)
15X-RAY DIFFRACTION15(chain C and resid 8:11)
16X-RAY DIFFRACTION16(chain C and resid 12:15)
17X-RAY DIFFRACTION17(chain D and resid 1:10)
18X-RAY DIFFRACTION18(chain D and resid 11:15)
19X-RAY DIFFRACTION19(chain D and resid 16:21)
20X-RAY DIFFRACTION20(chain D and resid 22:25)
21X-RAY DIFFRACTION21(chain D and resid 26:29)
22X-RAY DIFFRACTION22(chain D and resid 30:34)
23X-RAY DIFFRACTION23(chain D and resid 35:39)
24X-RAY DIFFRACTION24(chain D and resid 40:43)
25X-RAY DIFFRACTION25(chain D and resid 44:53)
26X-RAY DIFFRACTION26(chain D and resid 54:57)
27X-RAY DIFFRACTION27(chain D and resid 58:61)
28X-RAY DIFFRACTION28(chain E and resid 1:7)
29X-RAY DIFFRACTION29(chain E and resid 8:11)
30X-RAY DIFFRACTION30(chain E and resid 12:15)
31X-RAY DIFFRACTION31(chain F and resid 1:4)
32X-RAY DIFFRACTION32(chain F and resid 5:8)
33X-RAY DIFFRACTION33(chain F and resid 9:15)

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