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- PDB-5jrc: Crystal structure of NeC3PO in complex with ssRNA. -

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Basic information

Entry
Database: PDB / ID: 5jrc
TitleCrystal structure of NeC3PO in complex with ssRNA.
Components
  • (NEQ131) x 2
  • ssRNARNA
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
Biological speciesNanoarchaeum equitans (archaea)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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_conn_angle / pdbx_struct_oper_list / struct_conn / 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_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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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_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: ssRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,62710
Polymers105,4275
Non-polymers2005
Water3,927218
1
A: NEQ131
B: NEQ131
C: NEQ131
D: NEQ131
E: ssRNA
hetero molecules

A: NEQ131
B: NEQ131
C: NEQ131
D: NEQ131
E: ssRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,25420
Polymers210,85310
Non-polymers40110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area37210 Å2
ΔGint-286 kcal/mol
Surface area55460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.416, 77.648, 87.754
Angle α, β, γ (deg.)90.00, 118.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-323-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 18334 - 217
21BB0 - 18334 - 217
12AA0 - 18534 - 219
22CC0 - 18534 - 219
13AA0 - 18334 - 217
23DD0 - 18334 - 217
14BB0 - 18334 - 217
24CC0 - 18334 - 217
15BB0 - 18334 - 217
25DD0 - 18334 - 217
16CC0 - 18334 - 217
26DD0 - 18334 - 217

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein NEQ131


Mass: 25609.469 Da / Num. of mol.: 2
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.: 2 / 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: RNA chain ssRNA / RNA


Mass: 3247.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 10% (w/v) PEG 8000, 100 mM imidazole/HCl pH 8.0, 200 mM Ca(OAc)2

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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: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 71365 / % possible obs: 96.8 % / Redundancy: 4 % / Net I/σ(I): 16.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.07 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.505 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22983 3784 5 %RANDOM
Rwork0.20563 ---
obs0.20688 71365 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.236 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å2-0 Å2-1.46 Å2
2--4.2 Å20 Å2
3----2.87 Å2
Refinement stepCycle: 1 / Resolution: 1.9→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6190 133 5 218 6546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196464
X-RAY DIFFRACTIONr_bond_other_d0.0050.026260
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.9798715
X-RAY DIFFRACTIONr_angle_other_deg1.194314498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8545749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17425.235298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.984151304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2731527
X-RAY DIFFRACTIONr_chiral_restr0.0660.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026983
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021374
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_restr3.144312724
X-RAY DIFFRACTIONr_sphericity_free38.039562
X-RAY DIFFRACTIONr_sphericity_bonded12.153512759
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A116690.1
12B116690.1
21A115600.13
22C115600.13
31A115720.13
32D115720.13
41B112500.13
42C112500.13
51B116480.12
52D116480.12
61C111050.16
62D111050.16
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 272 -
Rwork0.353 5077 -
obs--94.71 %

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