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- PDB-5jre: Crystal structure of NeC3PO in complex with ssDNA. -

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Basic information

Entry
Database: PDB / ID: 5jre
TitleCrystal structure of NeC3PO in complex with ssDNA.
Components
  • NEQ131
  • ssDNADNA
KeywordsDNA BINDING PROTEIN / C3PO / complex
Function / homology
Function and homology information


sequence-specific DNA binding / metal ion binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2140 / Translin family / Translin superfamily / Translin family / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENINE / 9-METHYL-9H-PURIN-6-AMINE / DNA / NEQ131
Similarity search - Component
Biological speciesNanoarchaeum equitans (archaea)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGan, J. / Zhang, J.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structural basis for single-stranded RNA recognition and cleavage by C3PO
Authors: Zhang, J. / Liu, H. / Yao, Q. / Yu, X. / Chen, Y. / Cui, R. / Wu, B. / Zheng, L. / Zuo, J. / Huang, Z. / Ma, J. / Gan, J.
History
DepositionMay 6, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: 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 / citation / database_2 / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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: NEQ131
B: NEQ131
C: NEQ131
D: NEQ131
E: NEQ131
F: NEQ131
G: NEQ131
H: NEQ131
I: ssDNA
J: ssDNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,17318
Polymers211,05010
Non-polymers1,1238
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.830, 128.200, 102.180
Angle α, β, γ (deg.)90.00, 95.22, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTRPTRPAA0 - 18234 - 216
21SERSERTRPTRPBB0 - 18234 - 216
12SERSERLYSLYSAA0 - 18334 - 217
22SERSERLYSLYSCC0 - 18334 - 217
13SERSERLYSLYSAA0 - 18334 - 217
23SERSERLYSLYSDD0 - 18334 - 217
14GLYGLYSERSERAA-1 - 18433 - 218
24GLYGLYSERSEREE-1 - 18433 - 218
15SERSERTRPTRPAA0 - 18234 - 216
25SERSERTRPTRPFF0 - 18234 - 216
16SERSERLYSLYSAA0 - 18334 - 217
26SERSERLYSLYSGG0 - 18334 - 217
17SERSERLYSLYSAA0 - 18334 - 217
27SERSERLYSLYSHH0 - 18334 - 217
18SERSERTRPTRPBB0 - 18234 - 216
28SERSERTRPTRPCC0 - 18234 - 216
19SERSERTRPTRPBB0 - 18234 - 216
29SERSERTRPTRPDD0 - 18234 - 216
110SERSERTRPTRPBB0 - 18234 - 216
210SERSERTRPTRPEE0 - 18234 - 216
111SERSERLYSLYSBB0 - 18334 - 217
211SERSERLYSLYSFF0 - 18334 - 217
112SERSERTRPTRPBB0 - 18234 - 216
212SERSERTRPTRPGG0 - 18234 - 216
113SERSERTRPTRPBB0 - 18234 - 216
213SERSERTRPTRPHH0 - 18234 - 216
114SERSERLYSLYSCC0 - 18334 - 217
214SERSERLYSLYSDD0 - 18334 - 217
115SERSERLYSLYSCC0 - 18334 - 217
215SERSERLYSLYSEE0 - 18334 - 217
116SERSERTRPTRPCC0 - 18234 - 216
216SERSERTRPTRPFF0 - 18234 - 216
117SERSERLYSLYSCC0 - 18534 - 219
217SERSERLYSLYSGG0 - 18534 - 219
118SERSERLYSLYSCC0 - 18334 - 217
218SERSERLYSLYSHH0 - 18334 - 217
119SERSERLYSLYSDD0 - 18334 - 217
219SERSERLYSLYSEE0 - 18334 - 217
120SERSERTRPTRPDD0 - 18234 - 216
220SERSERTRPTRPFF0 - 18234 - 216
121SERSERLYSLYSDD0 - 18334 - 217
221SERSERLYSLYSGG0 - 18334 - 217
122SERSERSERSERDD0 - 18434 - 218
222SERSERSERSERHH0 - 18434 - 218
123SERSERTRPTRPEE0 - 18234 - 216
223SERSERTRPTRPFF0 - 18234 - 216
124SERSERLYSLYSEE0 - 18334 - 217
224SERSERLYSLYSGG0 - 18334 - 217
125SERSERLYSLYSEE0 - 18334 - 217
225SERSERLYSLYSHH0 - 18334 - 217
126SERSERTRPTRPFF0 - 18234 - 216
226SERSERTRPTRPGG0 - 18234 - 216
127SERSERTRPTRPFF0 - 18234 - 216
227SERSERTRPTRPHH0 - 18234 - 216
128SERSERLYSLYSGG0 - 18334 - 217
228SERSERLYSLYSHH0 - 18334 - 217

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
NEQ131


Mass: 25609.469 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanoarchaeum equitans (strain Kin4-M) (archaea)
Strain: Kin4-M / Gene: NEQ131 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74ML9
#2: DNA chain ssDNA / DNA


Mass: 3087.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Chemical
ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H5N5
#4: Chemical ChemComp-ADZ / 9-METHYL-9H-PURIN-6-AMINE


Mass: 149.153 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H7N5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 300, 0.1 M citric acid pH 4.2, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 137238 / % possible obs: 10.8 %

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 11.318 / SU ML: 0.133 / Cross valid method: THROUGHOUT / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 7234 5 %RANDOM
Rwork0.216 ---
obs0.218 137238 97.9 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 35.43 Å2
Baniso -1Baniso -2Baniso -3
1--4.57 Å20 Å2-0.06 Å2
2---0.37 Å2-0 Å2
3---4.86 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12247 131 83 348 12809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01912693
X-RAY DIFFRACTIONr_bond_other_d0.0060.0212294
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.97517079
X-RAY DIFFRACTIONr_angle_other_deg1.249328381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.82551474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33925.122574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.064152533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5061552
X-RAY DIFFRACTIONr_chiral_restr0.0620.21858
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213789
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022736
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.496324987
X-RAY DIFFRACTIONr_sphericity_free42.2125124
X-RAY DIFFRACTIONr_sphericity_bonded15.539524979
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A113650.07
12B113650.07
21A116120.08
22C116120.08
31A114560.09
32D114560.09
41A119230.07
42E119230.07
51A114550.08
52F114550.08
61A115400.1
62G115400.1
71A115040.1
72H115040.1
81B113260.09
82C113260.09
91B114280.08
92D114280.08
101B115450.08
102E115450.08
111B117930.07
112F117930.07
121B111740.11
122G111740.11
131B113430.1
132H113430.1
141C114760.1
142D114760.1
151C116190.09
152E116190.09
161C113360.09
162F113360.09
171C117920.08
172G117920.08
181C114510.11
182H114510.11
191D115730.09
192E115730.09
201D116080.09
202F116080.09
211D114710.11
212G114710.11
221D120220.08
222H120220.08
231E115400.09
232F115400.09
241E115740.09
242G115740.09
251E115830.1
252H115830.1
261F114450.1
262G114450.1
271F115010.1
272H115010.1
281G114930.11
282H114930.11
LS refinement shellResolution: 2.1→2.15 Å
RfactorNum. reflection% reflection
Rfree0.327 529 -
Rwork0.272 9861 -
obs--96.03 %

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