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- PDB-6m5b: X-ray crystal structure of cyclic-PIP and DNA complex in a revers... -

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Basic information

Entry
Database: PDB / ID: 6m5b
TitleX-ray crystal structure of cyclic-PIP and DNA complex in a reverse binding orientation
ComponentsDNA (5'-D(*CP*(CBR)P*AP*GP*GP*CP*CP*TP*GP*G)-3')
KeywordsDNA / PIP
Function / homologyChem-S7E / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.501 Å
AuthorsAbe, K. / Hirose, Y. / Eki, H. / Takeda, K. / Bando, T. / Endo, M. / Sugiyama, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)18KK0139 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)16H06356 Japan
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: X-ray Crystal Structure of a Cyclic-PIP-DNA Complex in the Reverse-Binding Orientation.
Authors: Abe, K. / Hirose, Y. / Eki, H. / Takeda, K. / Bando, T. / Endo, M. / Sugiyama, H.
History
DepositionMar 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*(CBR)P*AP*GP*GP*CP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8275
Polymers3,1251
Non-polymers7024
Water82946
1
A: DNA (5'-D(*CP*(CBR)P*AP*GP*GP*CP*CP*TP*GP*G)-3')
hetero molecules

A: DNA (5'-D(*CP*(CBR)P*AP*GP*GP*CP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,65410
Polymers6,2502
Non-polymers1,4048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation28_555x,-y,-z+1/21
Buried area3260 Å2
ΔGint-25 kcal/mol
Surface area3810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.235, 82.235, 82.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y,-z+1/2,x
#11: z,-x,-y+1/2
#12: -y+1/2,z,-x
#13: -z,-x+1/2,y
#14: -z+1/2,x,-y
#15: y,-z,-x+1/2
#16: x,-y,-z+1/2
#17: -x+1/2,y,-z
#18: -x,-y+1/2,z
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+1/4,-z+1/4,-y+1/4
#25: x+1/2,y+1/2,z+1/2
#26: x+3/4,-z+3/4,y+5/4
#27: x+3/4,z+5/4,-y+5/4
#28: z+3/4,y+5/4,-x+5/4
#29: -z+3/4,y+5/4,x+3/4
#30: -y+3/4,x+5/4,z+3/4
#31: y+3/4,-x+3/4,z+5/4
#32: z+1/2,x+1/2,y+1/2
#33: y+1/2,z+1/2,x+1/2
#34: -y+1/2,-z+1,x+1/2
#35: z+1/2,-x+1/2,-y+1
#36: -y+1,z+1/2,-x+1/2
#37: -z+1/2,-x+1,y+1/2
#38: -z+1,x+1/2,-y+1/2
#39: y+1/2,-z+1/2,-x+1
#40: x+1/2,-y+1/2,-z+1
#41: -x+1,y+1/2,-z+1/2
#42: -x+1/2,-y+1,z+1/2
#43: y+3/4,x+5/4,-z+5/4
#44: -y+3/4,-x+3/4,-z+3/4
#45: z+3/4,-y+3/4,x+5/4
#46: -z+3/4,-y+3/4,-x+3/4
#47: -x+3/4,z+5/4,y+3/4
#48: -x+3/4,-z+3/4,-y+3/4
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

21A-202-

HOH

31A-223-

HOH

41A-239-

HOH

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Components

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DNA chain , 1 types, 1 molecules A

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


Mass: 3124.888 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 5 types, 50 molecules

#2: Chemical ChemComp-S7E / 4-[[4-[(4-azanyl-1-methyl-pyrrol-2-yl)carbonylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-~{N}-[2-[[(3~{S})-3-azanyl-4-oxidanylidene-butyl]carbamoyl]-1-methyl-imidazol-4-yl]-1-methyl-imidazole-2-carboxamide


Mass: 592.610 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H32N12O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.71 Å3/Da / Density % sol: 66.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12.5% polyethylene glycol monomethyl ether 550, 2.5 mM magnesium chloride hexahydrate, 25 mM HEPES sodium, pH 7.0

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Data collection

DiffractionMean temperature: 16.7 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.91 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.5→41.118 Å / Num. obs: 14247 / % possible obs: 98.6 % / Redundancy: 14.328 % / Biso Wilson estimate: 23.982 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.054 / Χ2: 1.742 / Net I/σ(I): 26.37 / Num. measured all: 204128
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.592.5490.3931.735487234721530.7730.4891.7
1.59-1.75.7010.2644.5212503219321930.960.291100
1.7-1.8410.8710.17610.1821938201820180.9910.185100
1.84-2.0119.0640.14118.2236126189518950.9970.145100
2.01-2.2521.6020.10128.6536335168216820.9980.103100
2.25-2.5921.0150.07437.5731396149414940.9990.076100
2.59-3.1721.7160.0558.49277311277127710.051100
3.17-4.4621.3020.03682.052087698098010.037100
4.46-41.11821.1460.03585.721173655655510.03699.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.501→29.074 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1894 1056 7.42 %
Rwork0.184 13184 -
obs0.1845 14240 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 43.15 Å2 / Biso mean: 21.7689 Å2 / Biso min: 13.94 Å2
Refinement stepCycle: final / Resolution: 1.501→29.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 203 49 46 298
Biso mean--18.4 28.34 -
Num. residues----10
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.501-1.56920.31021450.296150291
1.5692-1.65190.25311000.24311683100
1.6519-1.75540.19161580.19921649100
1.7554-1.89090.22081490.18951645100
1.8909-2.08120.21851140.19071691100
2.0812-2.38220.26691330.20851659100
2.3822-3.00080.19151360.19391660100
3.0008-29.0740.13191210.15131695100

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