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- PDB-5a30: Crystal structure of mtPAP N472D mutant in complex with ATPgammaS -

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Basic information

Entry
Database: PDB / ID: 5a30
TitleCrystal structure of mtPAP N472D mutant in complex with ATPgammaS
ComponentsMITOCHONDRIAL PROTEINMitochondrion
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Mitochondrial poly(A) polymerase
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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)127,0056
Polymers125,9102
Non-polymers1,0954
Water905
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-79.6 kcal/mol
Surface area39340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.232, 95.220, 190.514
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: (-0.4252, 0.8301, -0.3607), (0.7745, 0.1274, -0.6197), (-0.4685, -0.5428, -0.6971)
Vector: 44.27, -45.92, -32.88)

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Components

#1: Protein MITOCHONDRIAL PROTEIN / Mitochondrion


Mass: 62955.078 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-568 / Mutation: YES
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSINGLE POINT MUTATION N472D

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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: 2.17 Å3/Da / Density % sol: 43.3 %
Description: RESOLUTION CUTOFF CRITERIA ACCORDING TO KARPLUS AND DIEDERICHS 2012

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. obs: 29303 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10 % / CC1/2: 0.99 / Rmerge(I) obs: 0.14 / Net I/σ(I): 15
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 1.7 / CC1/2: 0.57 / % possible all: 100

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Processing

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

Resolution: 2.75→39.75 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.89 / SU B: 18.521 / SU ML: 0.359 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28716 1484 5.1 %RANDOM
Rwork0.24689 ---
obs0.24894 27694 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.509 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--2.44 Å20 Å2
3----2.78 Å2
Refinement stepCycle: LAST / Resolution: 2.75→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7288 0 64 5 7357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197539
X-RAY DIFFRACTIONr_bond_other_d0.0020.027004
X-RAY DIFFRACTIONr_angle_refined_deg0.9761.97410247
X-RAY DIFFRACTIONr_angle_other_deg0.767316143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.275925
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79324.567335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.848151254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5791533
X-RAY DIFFRACTIONr_chiral_restr0.0530.21145
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218473
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021721
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_it2.6026.8763706
X-RAY DIFFRACTIONr_mcbond_other2.6026.8763705
X-RAY DIFFRACTIONr_mcangle_it4.28410.3064623
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.366.9793833
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: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 109 -
Rwork0.362 1971 -
obs--98.44 %

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