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- PDB-5a2z: Crystal structure of mtPAP in complex with GTP -

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Basic information

Entry
Database: PDB / ID: 5a2z
TitleCrystal structure of mtPAP in complex with GTP
ComponentsMITOCHONDRIAL PROTEINMitochondrion
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


mitochondrial 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 / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Mitochondrial poly(A) polymerase
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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: diffrn_detector / reflns / reflns_shell
Item: _diffrn_detector.type / _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
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)127,0036
Polymers125,9082
Non-polymers1,0954
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-78.9 kcal/mol
Surface area40150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.746, 94.364, 192.014
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: (-0.4289, 0.8324, 0.3509), (0.773, 0.1372, 0.6194), (0.4674, 0.5369, -0.7023)
Vector: -44, 45.85, -33.5)

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Components

#1: Protein MITOCHONDRIAL PROTEIN / Mitochondrion


Mass: 62954.094 Da / Num. of mol.: 2 / Fragment: 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-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.15 Å3/Da / Density % sol: 42.78 %
Description: RESOLUTION CUTOFF CRITERIA ACCORDING TO KARPLUS AND DIEDERICHS 2012

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 1
DetectorType: RAYONIX MX-225 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→40 Å / Num. obs: 40389 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.6
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.52 / % possible all: 98

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Processing

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

Resolution: 2.45→39.67 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.873 / SU B: 13.633 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R: 0.602 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29502 2025 5 %RANDOM
Rwork0.25987 ---
obs0.2616 38301 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.031 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2---0.06 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.45→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7348 0 47 20 7415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197569
X-RAY DIFFRACTIONr_bond_other_d0.0020.027151
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.97410264
X-RAY DIFFRACTIONr_angle_other_deg0.777316494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8325923
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71924.354333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.094151305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6151536
X-RAY DIFFRACTIONr_chiral_restr0.0510.21139
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218451
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021731
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_it1.6074.9833707
X-RAY DIFFRACTIONr_mcbond_other1.6074.9823706
X-RAY DIFFRACTIONr_mcangle_it2.8217.4684625
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2295.0493862
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: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 154 -
Rwork0.358 2736 -
obs--97.21 %

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