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- PDB-4lt6: Crystal Structure of human poly(A) polymerase gamma -

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Basic information

Entry
Database: PDB / ID: 4lt6
TitleCrystal Structure of human poly(A) polymerase gamma
ComponentsPoly(A) polymerase gamma
KeywordsTRANSFERASE / Poly(A) polymerase / PAP / polymerase / polyadenylation / 3' processing / mRNA processing / Nucleus
Function / homology
Function and homology information


: / : / polynucleotide adenylyltransferase / : / nuclear body / RNA binding / nucleoplasm / ATP binding / membrane / metal ion binding ...: / : / polynucleotide adenylyltransferase / : / nuclear body / RNA binding / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol
Similarity search - Function
Poly(A) polymerase, RNA-binding domain / Poly(A) polymerase, central domain / Poly(A) polymerase predicted RNA binding domain / Poly(A) polymerase central domain / Poly(a)-polymerase, middle domain - #10 / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal / Poly(a)-polymerase, middle domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain ...Poly(A) polymerase, RNA-binding domain / Poly(A) polymerase, central domain / Poly(A) polymerase predicted RNA binding domain / Poly(A) polymerase central domain / Poly(a)-polymerase, middle domain - #10 / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal / Poly(a)-polymerase, middle domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / Poly(A) polymerase gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsYang, Q. / Nausch, L. / Martin, G. / Keller, W. / Doublie, S.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Crystal structure of human poly(a) polymerase gamma reveals a conserved catalytic core for canonical poly(a) polymerases.
Authors: Yang, Q. / Nausch, L.W. / Martin, G. / Keller, W. / Doublie, S.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _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_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(A) polymerase gamma
B: Poly(A) polymerase gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6426
Polymers118,5792
Non-polymers1,0634
Water95553
1
A: Poly(A) polymerase gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8213
Polymers59,2901
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly(A) polymerase gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8213
Polymers59,2901
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.870, 89.920, 201.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Poly(A) polymerase gamma / PAP-gamma / Neo-poly(A) polymerase / Neo-PAP / Polynucleotide adenylyltransferase gamma / SRP RNA ...PAP-gamma / Neo-poly(A) polymerase / Neo-PAP / Polynucleotide adenylyltransferase gamma / SRP RNA 3'-adenylating enzyme


Mass: 59289.688 Da / Num. of mol.: 2 / Fragment: UNP residues 1-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAPOLG, PAP2, PAPG / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BWT3, polynucleotide adenylyltransferase
#2: Chemical ChemComp-3AT / 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / CORDYCEPIN TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20%(W/V) PEG 8000, 50mM Tris-HCl, 100mM (NH4)2SO4, 5mM CaCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 19, 2003
RadiationMonochromator: Xenocs mirrors / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.79→20 Å / Num. all: 32026 / Num. obs: 31418 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.79-2.97189.5
2.97-3.2199.4
3.2-3.521100
3.52-4.031100
4.03-5.061100
5.06-20199.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6_289)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q78

1q78


Resolution: 2.79→19.884 Å / SU ML: 0.41 / σ(F): 1.35 / Phase error: 27.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 2784 4.84 %
Rwork0.193 --
obs0.1962 29444 95.66 %
all-32026 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.8225 Å20 Å2-0 Å2
2---0.1153 Å20 Å2
3----6.7072 Å2
Refinement stepCycle: LAST / Resolution: 2.79→19.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7529 0 62 53 7644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097777
X-RAY DIFFRACTIONf_angle_d1.2510564
X-RAY DIFFRACTIONf_dihedral_angle_d17.9052914
X-RAY DIFFRACTIONf_chiral_restr0.0851175
X-RAY DIFFRACTIONf_plane_restr0.0071336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.8360.3748680.3151861X-RAY DIFFRACTION64
2.836-2.88750.37741130.28052326X-RAY DIFFRACTION81
2.8875-2.94280.3361270.28472463X-RAY DIFFRACTION88
2.9428-3.00270.32491380.28092676X-RAY DIFFRACTION92
3.0027-3.06780.31351290.25342709X-RAY DIFFRACTION95
3.0678-3.13880.33351310.26272824X-RAY DIFFRACTION98
3.1388-3.2170.30711730.26212829X-RAY DIFFRACTION99
3.217-3.30360.39521450.25942815X-RAY DIFFRACTION99
3.3036-3.40040.36221630.24172831X-RAY DIFFRACTION100
3.4004-3.50960.27261590.22582831X-RAY DIFFRACTION100
3.5096-3.63430.26671440.21172894X-RAY DIFFRACTION100
3.6343-3.77880.26931300.18132878X-RAY DIFFRACTION100
3.7788-3.94950.22581330.1652854X-RAY DIFFRACTION100
3.9495-4.1560.20041530.16062840X-RAY DIFFRACTION100
4.156-4.41370.24581200.15392880X-RAY DIFFRACTION100
4.4137-4.75020.21251630.14832858X-RAY DIFFRACTION100
4.7502-5.22030.22171520.14852858X-RAY DIFFRACTION100
5.2203-5.95790.20751670.16162852X-RAY DIFFRACTION100
5.9579-7.44040.2121380.17042871X-RAY DIFFRACTION100
7.4404-19.88470.18261380.14912825X-RAY DIFFRACTION99

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