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- PDB-1txz: Crystal structure of yeast ymx7, an ADP-ribose-1''-monophosphatas... -

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Basic information

Entry
Database: PDB / ID: 1txz
TitleCrystal structure of yeast ymx7, an ADP-ribose-1''-monophosphatase, complexed with ADP-ribose
ComponentsHypothetical 32.1 kDa protein in ADH3-RCA1 intergenic region
Keywordsstructural genomics / unknown function / Dimer / Two domain organization / ADP-Ribose complex / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


tRNA splicing, via endonucleolytic cleavage and ligation / ADP-ribose 1''-phosphate phosphatase / hydrolase activity
Similarity search - Function
Macro-like domain / Macro-like domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / Probable ADP-ribose 1''-phosphate phosphatase YML087W
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier / Resolution: 2.05 Å
AuthorsKumaran, D. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Protein Sci. / Year: 2005
Title: Structure and mechanism of ADP-ribose-1''-monophosphatase (Appr-1''-pase), a ubiquitous cellular processing enzyme.
Authors: Kumaran, D. / Eswaramoorthy, S. / Studier, F.W. / Swaminathan, S.
History
DepositionJul 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 3, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.ptnr1_auth_comp_id ..._audit_author.identifier_ORCID / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 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: Hypothetical 32.1 kDa protein in ADH3-RCA1 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9436
Polymers32,1061
Non-polymers8375
Water1,56787
1
A: Hypothetical 32.1 kDa protein in ADH3-RCA1 intergenic region
hetero molecules

A: Hypothetical 32.1 kDa protein in ADH3-RCA1 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,88512
Polymers64,2122
Non-polymers1,67310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area6610 Å2
ΔGint-120 kcal/mol
Surface area20700 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)107.437, 37.931, 62.514
Angle α, β, γ (deg.)90.00, 112.30, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the crystallographic two fold axis

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hypothetical 32.1 kDa protein in ADH3-RCA1 intergenic region / YMX7


Mass: 32106.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YMR087W, YM9582.12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04299

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Non-polymers , 5 types, 92 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1.84 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG 6000, Citric acid, Ethylene glycol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Feb 20, 2003 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 14181 / Num. obs: 14181 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 22.8
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.16 / Num. unique all: 1010 / % possible all: 69.2

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Processing

Software
NameClassification
CBASSdata collection
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
RefinementMethod to determine structure: Difference Fourier
Starting model: pdb entry 1NJR

1njr


Resolution: 2.05→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.235 1105 Random
Rwork0.2 --
all-13851 -
obs-13851 -
Displacement parametersBiso mean: 46.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.33 Å20 Å2-10.056 Å2
2--8.102 Å20 Å2
3----4.772 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 51 87 2115
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.52
LS refinement shellResolution: 2.05→2.08 Å /
RfactorNum. reflection
Rfree0.33 30
Rwork0.25 -
obs-345

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