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- PDB-6umq: Structure of DUF89 -

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Basic information

Entry
Database: PDB / ID: 6umq
TitleStructure of DUF89
ComponentsDamage-control phosphatase DUF89
KeywordsTRANSFERASE / Metabolite repair / DUF89
Function / homology
Function and homology information


protein carboxyl O-methyltransferase activity / protein-glutamate O-methyltransferase activity / fructose 6-phosphate aldolase activity / fructose-1-phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / S-adenosylmethionine-dependent methyltransferase activity / phosphatase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / DNA damage response ...protein carboxyl O-methyltransferase activity / protein-glutamate O-methyltransferase activity / fructose 6-phosphate aldolase activity / fructose-1-phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / S-adenosylmethionine-dependent methyltransferase activity / phosphatase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / DNA damage response / enzyme binding / metal ion binding
Similarity search - Function
Transcription Elongation Factor S-II; Chain A - #60 / Damage-control phosphatase ARMT1 / Damage-control phosphatase ARMT1-like, metal-binding domain / Damage-control phosphatase ARMT1-like, metal-binding domain superfamily / Damage-control phosphatase ARMT1-like domain / Transcription Elongation Factor S-II; Chain A / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Damage-control phosphatase ARMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPerry, J.J. / Kenjic, N. / Dennis, T.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1714569 United States
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Human ARMT1 structure and substrate specificity indicates that it is a DUF89 family damage-control phosphatase.
Authors: Dennis, T.N. / Kenjic, N. / Kang, A.S. / Lowenson, J.D. / Kirkwood, J.S. / Clarke, S.G. / Perry, J.J.P.
History
DepositionOct 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Damage-control phosphatase DUF89
B: Damage-control phosphatase DUF89
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,5596
Polymers102,4622
Non-polymers974
Water10,359575
1
A: Damage-control phosphatase DUF89
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2803
Polymers51,2311
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Damage-control phosphatase DUF89
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2803
Polymers51,2311
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.140, 194.473, 114.201
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Damage-control phosphatase DUF89 / Acidic residue methyltransferase 1 / Protein-glutamate O-methyltransferase / Sugar phosphate phosphatase ARMT1


Mass: 51231.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARMT1, C6orf211 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H993, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 18% PEG 4000, 200mM MgCl2, 100mM Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.84→66.49 Å / Num. obs: 85552 / % possible obs: 98.54 % / Redundancy: 6.1 % / Biso Wilson estimate: 14.26 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.4
Reflection shellResolution: 1.85→1.916 Å / Rmerge(I) obs: 0.215 / Num. unique obs: 8480 / % possible all: 99.27

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PT1

3pt1


Resolution: 1.85→66.49 Å / SU ML: 0.1745 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.4558
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.224 1975 2.34 %
Rwork0.1964 82420 -
obs0.1971 84395 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.26 Å2
Refinement stepCycle: LAST / Resolution: 1.85→66.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6878 0 4 575 7457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01417094
X-RAY DIFFRACTIONf_angle_d1.21549630
X-RAY DIFFRACTIONf_chiral_restr0.06341030
X-RAY DIFFRACTIONf_plane_restr0.00831214
X-RAY DIFFRACTIONf_dihedral_angle_d21.572580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.27131410.21695849X-RAY DIFFRACTION99.34
1.9-1.950.25251420.19675867X-RAY DIFFRACTION98.93
1.95-20.23241410.18745854X-RAY DIFFRACTION99.03
2-2.070.2361400.18455878X-RAY DIFFRACTION99.11
2.07-2.140.21111400.1925891X-RAY DIFFRACTION99.01
2.14-2.230.26621400.18635808X-RAY DIFFRACTION98.35
2.23-2.330.22411400.18735852X-RAY DIFFRACTION98.49
2.33-2.450.21351430.19125843X-RAY DIFFRACTION98.42
2.45-2.610.22721390.19225833X-RAY DIFFRACTION97.92
2.61-2.810.20741380.19695843X-RAY DIFFRACTION97.92
2.81-3.090.19911420.19725861X-RAY DIFFRACTION98.04
3.09-3.540.24151420.19425958X-RAY DIFFRACTION99.06
3.54-4.460.19541420.18475968X-RAY DIFFRACTION98.39

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