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- PDB-1njr: Crystal structure of yeast ymx7, an ADP-ribose-1''-monophosphatase -

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Basic information

Entry
Database: PDB / ID: 1njr
TitleCrystal structure of yeast ymx7, an ADP-ribose-1''-monophosphatase
Components32.1 kDa protein in ADH3-RCA1 intergenic region
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Dimer / Two domain organization / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


ADP-ribose 1''-phosphate phosphatase / tRNA splicing, via endonucleolytic cleavage and ligation / phosphatase 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
Xylitol / Probable ADP-ribose 1''-phosphate phosphatase YML087W
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsKumaran, D. / Eswaramoorthy, S. / Studier, F.W. / 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
DepositionJan 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 3, 2021Group: Structure summary / Category: audit_author / chem_comp
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms
Remark 300BIOMOLECULE: DIMER THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ...BIOMOLECULE: DIMER THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL DIMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,7272
Polymers32,5751
Non-polymers1521
Water2,018112
1
A: 32.1 kDa protein in ADH3-RCA1 intergenic region
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)65,4554
Polymers65,1502
Non-polymers3042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3660 Å2
ΔGint-16 kcal/mol
Surface area21860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)107.694, 38.149, 64.736
Angle α, β, γ (deg.)90.00, 112.21, 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

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


Mass: 32575.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YMR087W or YM9582.12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04299
#2: Sugar ChemComp-XYL / Xylitol / D-Xylitol / Xylitol


Type: D-saccharide / Mass: 152.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H12O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 1.89 Å3/Da / Density % sol: 34.91 %
Description: High resolution data for this structure was collected at X25 of NSLS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG 6000, Citric acid, Xylitol, 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: X25 / Wavelength: 0.979 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Sep 24, 2002 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 18988 / Num. obs: 18988 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 46.9 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 18.3
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.266 / Num. unique all: 1620 / % possible all: 84

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Processing

Software
NameClassification
MARMADdata collection
HKL-2000data reduction
SOLVEphasing
SHARPphasing
DMmodel building
CNSrefinement
MARMADdata reduction
HKL-2000data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1288 -random
Rwork0.206 ---
all-18720 --
obs-18720 96 %-
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 10 112 2099
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.201

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