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- PDB-5a2v: Crystal structure of mtPAP in Apo form -

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Basic information

Entry
Database: PDB / ID: 5a2v
TitleCrystal structure of mtPAP in Apo form
ComponentsMITOCHONDRIAL PROTEIN
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


mitochondrial RNA 3'-end processing / RNA 3'-end processing / histone mRNA catabolic process / poly(A) RNA polymerase activity / UTP binding / manganese ion binding / GTP binding / magnesium ion binding / protein homodimerization activity / mitochondrion ...mitochondrial RNA 3'-end processing / RNA 3'-end processing / histone mRNA catabolic process / poly(A) RNA polymerase activity / UTP binding / manganese ion binding / GTP binding / magnesium ion binding / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding
Similarity search - Function
RL domain / RL domain / TUTase nucleotidyltransferase domain / PAP/25A-associated / Cid1 family poly A polymerase / : / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Mitochondrial poly(A) polymerase
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsLapkouski, M. / Hallberg, B.M.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structure of Mitochondrial Poly(A) RNA Polymerase Reveals the Structural Basis for Dimerization, ATP Selectivity and the Spax4 Disease Phenotype.
Authors: Lapkouski, M. / Hallberg, B.M.
History
DepositionMay 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MITOCHONDRIAL PROTEIN
B: MITOCHONDRIAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,0506
Polymers125,9082
Non-polymers1424
Water12,052669
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-91.9 kcal/mol
Surface area41450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.391, 94.367, 191.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.4459, 0.8189, -0.3613), (0.7647, 0.1387, -0.6293), (-0.4652, -0.5569, -0.688)
Vector: 44.24, -46.23, -33.22)

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Components

#1: Protein MITOCHONDRIAL PROTEIN


Mass: 62954.094 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 37-568
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: F1NBW0
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.39 % / Description: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→40 Å / Num. obs: 97579 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Net I/σ(I): 17
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 13 % / Rmerge(I) obs: 2.04 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.54 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.82→38 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.688 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24532 4876 5 %RANDOM
Rwork0.22212 ---
obs0.22328 92603 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.321 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.82→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7421 0 4 669 8094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197763
X-RAY DIFFRACTIONr_bond_other_d0.0020.027318
X-RAY DIFFRACTIONr_angle_refined_deg0.9161.96310567
X-RAY DIFFRACTIONr_angle_other_deg0.805316919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9865992
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55724.726347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.563151350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6071532
X-RAY DIFFRACTIONr_chiral_restr0.0540.21182
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218816
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021782
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_it1.0153.2533820
X-RAY DIFFRACTIONr_mcbond_other1.0153.2523819
X-RAY DIFFRACTIONr_mcangle_it1.8314.874782
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8493.3023943
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
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 346 -
Rwork0.351 6804 -
obs--99.96 %

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