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- PDB-5jr9: Crystal structure of apo-NeC3PO -

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Basic information

Entry
Database: PDB / ID: 5jr9
TitleCrystal structure of apo-NeC3PO
Components(NEQ131) x 3
KeywordsDNA BINDING PROTEIN / C3PO / open form
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
Biological speciesNanoarchaeum equitans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZhang, J. / Gan, 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


Theoretical massNumber of molelcules
Total (without water)204,0438
Polymers204,0438
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27640 Å2
ΔGint-188 kcal/mol
Surface area59840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.438, 92.712, 92.745
Angle α, β, γ (deg.)114.29, 113.39, 95.76
Int Tables number1
Space group name H-MP1
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
11GLYGLYLYSLYSAA-1 - 18333 - 217
21GLYGLYLYSLYSBB-1 - 18333 - 217
12METMETSERSERAA1 - 18435 - 218
22METMETSERSERCC1 - 18435 - 218
13SERSERLYSLYSAA0 - 18334 - 217
23SERSERLYSLYSDD0 - 18334 - 217
14GLYGLYLYSLYSAA-1 - 18333 - 217
24GLYGLYLYSLYSEE-1 - 18333 - 217
15SERSERLYSLYSAA0 - 18334 - 217
25SERSERLYSLYSFF0 - 18334 - 217
16GLYGLYLYSLYSAA-1 - 18333 - 217
26GLYGLYLYSLYSGG-1 - 18333 - 217
17SERSERLYSLYSAA0 - 18334 - 217
27SERSERLYSLYSHH0 - 18334 - 217
18METMETLYSLYSBB1 - 18335 - 217
28METMETLYSLYSCC1 - 18335 - 217
19SERSERLYSLYSBB0 - 18334 - 217
29SERSERLYSLYSDD0 - 18334 - 217
110GLYGLYSERSERBB-1 - 18433 - 218
210GLYGLYSERSEREE-1 - 18433 - 218
111SERSERLYSLYSBB0 - 18334 - 217
211SERSERLYSLYSFF0 - 18334 - 217
112GLYGLYSERSERBB-1 - 18433 - 218
212GLYGLYSERSERGG-1 - 18433 - 218
113SERSERLYSLYSBB0 - 18334 - 217
213SERSERLYSLYSHH0 - 18334 - 217
114METMETLYSLYSCC1 - 18335 - 217
214METMETLYSLYSDD1 - 18335 - 217
115METMETLYSLYSCC1 - 18335 - 217
215METMETLYSLYSEE1 - 18335 - 217
116METMETLYSLYSCC1 - 18335 - 217
216METMETLYSLYSFF1 - 18335 - 217
117METMETLYSLYSCC1 - 18335 - 217
217METMETLYSLYSGG1 - 18335 - 217
118METMETLYSLYSCC1 - 18335 - 217
218METMETLYSLYSHH1 - 18335 - 217
119SERSERLYSLYSDD0 - 18334 - 217
219SERSERLYSLYSEE0 - 18334 - 217
120SERSERSERSERDD0 - 18434 - 218
220SERSERSERSERFF0 - 18434 - 218
121SERSERLYSLYSDD0 - 18334 - 217
221SERSERLYSLYSGG0 - 18334 - 217
122SERSERSERSERDD0 - 18434 - 218
222SERSERSERSERHH0 - 18434 - 218
123SERSERLYSLYSEE0 - 18334 - 217
223SERSERLYSLYSFF0 - 18334 - 217
124GLYGLYSERSEREE-1 - 18433 - 218
224GLYGLYSERSERGG-1 - 18433 - 218
125SERSERLYSLYSEE0 - 18334 - 217
225SERSERLYSLYSHH0 - 18334 - 217
126SERSERLYSLYSFF0 - 18334 - 217
226SERSERLYSLYSGG0 - 18334 - 217
127SERSERSERSERFF0 - 18434 - 218
227SERSERSERSERHH0 - 18434 - 218
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: 25551.367 Da / Num. of mol.: 1 / Fragment: UNP residues 1-184
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: Protein
NEQ131


Mass: 25480.289 Da / Num. of mol.: 6 / Fragment: UNP residues 1-184
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
#3: Protein NEQ131


Mass: 25609.469 Da / Num. of mol.: 1
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 5% v/v tacsimate (pH 7.0), 0.1 M HEPES (pH 7.0), 10% w/v PEG monomethyl ether 5,000

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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: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 80578 / % possible obs: 95.4 % / Redundancy: 2.5 % / Net I/σ(I): 16.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.703 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25157 4260 5 %RANDOM
Rwork0.22863 ---
obs0.2298 80578 95.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.604 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20.56 Å23.68 Å2
2---3.68 Å20.14 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12234 0 0 52 12286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212442
X-RAY DIFFRACTIONr_bond_other_d0.0060.0212049
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.99516725
X-RAY DIFFRACTIONr_angle_other_deg1.321327853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.14751478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.71225.445584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79152495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1071545
X-RAY DIFFRACTIONr_chiral_restr0.0740.21836
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213673
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022632
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A118490.08
12B118490.08
21A115420.06
22C115420.06
31A108300.08
32D108300.08
41A120370.06
42E120370.06
51A119410.07
52F119410.07
61A119820.07
62G119820.07
71A116100.07
72H116100.07
81B113750.08
82C113750.08
91B108250.08
92D108250.08
101B118790.08
102E118790.08
111B118120.07
112F118120.07
121B119840.07
122G119840.07
131B115620.07
132H115620.07
141C107250.08
142D107250.08
151C116720.07
152E116720.07
161C114250.08
162F114250.08
171C116560.07
172G116560.07
181C112750.07
182H112750.07
191D109480.07
192E109480.07
201D108990.08
202F108990.08
211D109600.08
212G109600.08
221D107360.09
222H107360.09
231E117790.08
232F117790.08
241E120210.08
242G120210.08
251E114520.09
252H114520.09
261F119590.07
262G119590.07
271F116350.07
272H116350.07
281G116120.06
282H116120.06
LS refinement shellResolution: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 300 -
Rwork0.354 5571 -
obs--89.47 %

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