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- PDB-4xic: ANTPHD WITH 15BP di-thioate modified DNA DUPLEX -

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Basic information

Entry
Database: PDB / ID: 4xic
TitleANTPHD WITH 15BP di-thioate modified DNA DUPLEX
Components
  • DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C2S)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 / DNA Binding / Methylated DNA / ZINC FINGER / TRANSCRIPTION / Transcription Regulator-DNA complex
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: 2.69 Å
AuthorsWhite, M.A. / Zandarashvili, L. / Iwahara, J.
Citation
Journal: Biophys.J. / Year: 2015
Title: Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate.
Authors: Zandarashvili, L. / Nguyen, D. / Anderson, K.M. / White, M.A. / Gorenstein, D.G. / Iwahara, J.
#1: Journal: Genes Dev. / Year: 2014
Title: Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence.
Authors: Hashimoto, H. / Olanrewaju, Y.O. / Zheng, Y. / Wilson, G.G. / Zhang, X. / Cheng, X.
History
DepositionJan 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Data collection
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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*(C2S)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*(C2S)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)34,87112
Polymers34,3416
Non-polymers5316
Water25214
1
A: Homeotic protein antennapedia
B: DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C2S)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)17,3475
Polymers17,1703
Non-polymers1772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-21 kcal/mol
Surface area8420 Å2
MethodPISA
2
D: Homeotic protein antennapedia
E: DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C2S)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)17,5247
Polymers17,1703
Non-polymers3544
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-36 kcal/mol
Surface area8440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.539, 96.539, 89.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Homeotic protein antennapedia / Homeosis


Mass: 7961.297 Da / Num. of mol.: 2 / Fragment: UNP residues 297-356
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

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain DNA (5'-D(*AP*GP*AP*AP*AP*GP*CP*(C2S)P*AP*TP*TP*AP*GP*AP*G)-3')


Mass: 4683.193 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)

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Non-polymers , 3 types, 20 molecules

#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: 20 mM BTP, 10 mM NiCl, 5% MPD / PH range: 7

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.69→40 Å / Num. obs: 18508 / % possible obs: 99.8 % / Redundancy: 8.9 % / Biso Wilson estimate: 46.64 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.043 / Rrim(I) all: 0.134 / Χ2: 1 / Net I/av σ(I): 16.154 / Net I/σ(I): 10.5 / Num. measured all: 109936
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Χ2% possible allRpim(I) allRmerge(I) obsRrim(I) all
2.7-2.755.86020.3740.935100
2.75-2.85.95930.4140.9381000.921
2.8-2.855.86040.5910.9281000.745
2.85-2.915.95950.610.9331000.678
2.91-2.975.96050.6380.9361000.572
2.97-3.046.16030.8870.86499.80.3370.7790.851
3.04-3.126.36040.9580.8591000.2540.6130.664
3.12-3.26.85960.9960.8081000.1230.3080.332
3.2-3.37.26030.9960.86598.90.0860.220.237
3.3-3.47.76070.9960.8699.70.0720.1890.203
3.4-3.528.36020.9960.8651000.0880.2470.263
3.52-3.669.16180.9910.8791000.0960.2790.295
3.66-3.839.96040.990.9371000.0740.2220.235
3.83-4.0311.56260.9891.071000.0680.2210.231
4.03-4.2813.16140.991.1471000.0610.2170.226
4.28-4.6213.36220.9941.1541000.0480.170.177
4.62-5.0813.26320.9911.1451000.0420.1460.152
5.08-5.8112.96280.9941.1241000.0350.1240.129
5.81-7.3112.46480.9941.051000.0330.1110.116
7.31-4010.37030.9940.9998.60.0320.0880.094

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Processing

Software
NameVersionClassification
PHENIXdev_1810refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4XID

4xid


Resolution: 2.69→37.439 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 988 5.34 %Random
Rwork0.216 ---
obs0.2189 18507 82.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→37.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 1218 27 14 2299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062486
X-RAY DIFFRACTIONf_angle_d0.8233606
X-RAY DIFFRACTIONf_dihedral_angle_d28.6471032
X-RAY DIFFRACTIONf_chiral_restr0.043385
X-RAY DIFFRACTIONf_plane_restr0.041274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6902-2.83190.3988480.3612919X-RAY DIFFRACTION30
2.8319-3.00930.36951040.36641883X-RAY DIFFRACTION62
3.0093-3.24150.35351550.27712695X-RAY DIFFRACTION89
3.2415-3.56750.30091600.2252967X-RAY DIFFRACTION97
3.5675-4.08320.28781780.19863017X-RAY DIFFRACTION100
4.0832-5.14230.24221710.19173025X-RAY DIFFRACTION100
5.1423-37.44220.21651720.18253013X-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)
10.1231-0.08750.04060.0637-0.03310.05970.08840.0696-0.22960.05240.0914-0.15730.1830.07730.2990.54420.02330.10.079-0.08880.37670.1818-29.459627.2674
20.0273-0.0202-0.00130.02450.01980.0325-0.02570.0084-0.00120.0364-0.0047-0.01050.007-0.02390.00440.2758-0.0434-0.08560.0868-0.06950.1525-0.4638-15.937926.6569
30.02210.0047-0.00790.0047-0.01020.02530.0116-0.01430.0207-0.0290.0259-0.0317-0.00540.02940.02630.41550.1366-0.03770.1622-0.14790.30967.6602-22.894926.6018
40.00560.01030.01150.03680.0240.0415-0.01550.0132-0.0081-0.01740.00120.02550.0269-0.01990.00260.3688-0.09620.02190.0829-0.03760.1145-1.9441-24.319321.0801
50.0056-0.0034-0.00130.0020.00030.00480.02080.0096-0.0025-0.01840.02650.03590.0215-0.03600.6642-0.26280.05520.7129-0.08290.7495-14.147-26.785419.2626
60.0767-0.04950.03830.0317-0.0280.1159-0.01140.0978-0.0054-0.0096-0.0282-0.01890.0325-0.0073-0.08310.3115-0.08590.12850.22320.0790.17093.7818-6.074310.3807
70.2976-0.05920.02310.0182-0.01080.00740.00740.0066-0.074-0.0546-0.00710.10060.0384-0.0222-0.03570.362-0.20920.0690.1759-0.10790.2845-4.5723-18.217713.2377
80.1385-0.09680.03140.3166-0.10490.0362-0.09080.0403-0.0933-0.0154-0.10270.08510.1238-0.107-0.15731.1203-0.0487-0.00110.4236-0.2660.69280.7598-36.396211.3963
90.0199-0.0147-0.00290.0181-0.00190.00270.0217-0.00790.0053-0.0303-0.03550.01670.0934-0.05720.01660.7701-0.0458-0.06440.4064-0.30480.8382-3.9273-45.548714.7196
100.0095-0.0035-0.00630.01740.0090.0064-0.0004-0.00080.0165-0.02680.0192-0.0225-0.02220.01460.09620.5385-0.04680.04510.1855-0.15340.24551.4327-31.248815.6588
110.20450.16070.15630.37920.25330.2153-0.15960.05640.0577-0.1494-0.0986-0.02710.11850.1346-0.0930.7202-0.039-0.02230.24060.02110.2347-2.7689-14.75017.9863
120.032-0-0.01530.03080.00120.05820.00550.00440.0038-0.0407-0.0043-0.0185-0.00570.02180.00840.3190.08210.04560.73490.08030.2396-13.3483.552242.3182
130.1936-0.0999-0.10160.05370.04640.06520.01950.01780.0486-0.00350.031-0.0299-0.0124-0.00030.16730.08910.08810.01690.5703-0.07280.1288-20.988-4.245748.1865
140.01430.0162-0.0080.0173-0.00910.00420.02040.1023-0.0073-0.0240.00470.0615-0.0089-0.06580.11710.19920.1056-0.01940.807-0.12110.3253-29.30090.127744.2215
150.0631-0.01560.02280.003-0.00520.0072-0.00460.05580.0224-0.0308-0.03290.0272-0.0279-0.0444-0.08980.14610.129-0.06960.7864-0.05110.1811-23.58-3.0137.0012
160.01610.00050.00040.0028-0.00040.002-0.0072-0.0007-0.0090.0162-0.0170.01740.01650.0238-00.94690.0793-0.02991.0895-0.28480.7856-19.4023-17.050137.9804
170.14570.0167-0.0280.0246-0.00660.0059-0.0035-0.00230.0243-0.00590.0008-0.0112-0.03290.02660.10390.40010.0366-0.39251.20650.011.0172-42.19451.602526.6931
180.06690.0478-0.01190.0486-0.03090.0375-0.0990.0391-0.00550.03360.0112-0.0812-0.0537-0.0506-0.04870.44770.1661-0.111.6672-0.35090.7743-27.8379-7.682828.8197
190.0128-0.0129-0.02060.0356-0.03150.1498-0.07640.20110.0507-0.0062-0.0088-0.1038-0.08290.0027-0.00170.30470.0818-0.0820.87920.04430.3043-10.36560.204228.0048
200.09340.0327-0.05280.036-0.03860.0465-0.0157-0.025-0.05910.03110.00850.11640.028-0.0641-0.0560.0993-0.11820.06520.3034-0.02440.1887-2.7564-6.065731.1662
210.0351-0.04550.01160.0824-0.01430.0044-0.00250.01720.0011-0.01550.01650.0278-0.0258-0.03270.06590.20160.1258-0.08920.86280.00040.3347-17.2114-0.095931.6911
220.6269-0.1307-0.25690.13730.03220.1113-0.20860.0401-0.0292-0.0157-0.16360.0451-0.276-0.0716-0.06730.6271-0.0048-0.26042.0289-0.06550.8888-33.4772-5.557524.5839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:23)
2X-RAY DIFFRACTION2(chain A and resid 24:33)
3X-RAY DIFFRACTION3(chain A and resid 34:43)
4X-RAY DIFFRACTION4(chain A and resid 44:53)
5X-RAY DIFFRACTION5(chain A and resid 54:60)
6X-RAY DIFFRACTION6(chain B and resid 0:3)
7X-RAY DIFFRACTION7(chain B and resid 4:7)
8X-RAY DIFFRACTION8(chain B and resid 8:14)
9X-RAY DIFFRACTION9(chain C and resid 23:26)
10X-RAY DIFFRACTION10(chain C and resid 27:30)
11X-RAY DIFFRACTION11(chain C and resid 31:37)
12X-RAY DIFFRACTION12(chain D and resid 5:10)
13X-RAY DIFFRACTION13(chain D and resid 11:22)
14X-RAY DIFFRACTION14(chain D and resid 23:40)
15X-RAY DIFFRACTION15(chain D and resid 41:55)
16X-RAY DIFFRACTION16(chain D and resid 56:60)
17X-RAY DIFFRACTION17(chain E and resid 0:3)
18X-RAY DIFFRACTION18(chain E and resid 4:8)
19X-RAY DIFFRACTION19(chain E and resid 9:14)
20X-RAY DIFFRACTION20(chain F and resid 23:26)
21X-RAY DIFFRACTION21(chain F and resid 27:30)
22X-RAY DIFFRACTION22(chain F and resid 31:37)

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