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- PDB-1yqe: Crystal Structure of Conserved Protein of Unknown Function AF0625 -

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Basic information

Entry
Database: PDB / ID: 1yqe
TitleCrystal Structure of Conserved Protein of Unknown Function AF0625
ComponentsHypothetical UPF0204 protein AF0625
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / AF0625 / Sulfur SAD / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


D-aminoacyl-tRNA deacylase activity / D-aminoacyl-tRNA deacylase / D-amino acid catabolic process / zinc ion binding
Similarity search - Function
AF0625-like / AF0625-like / D-aminoacyl-tRNA deacylase DtdA / D-aminoacyl-tRNA deacylase, archaea / D-aminoacyl-tRNA deacylase / Aminopeptidase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYROPHOSPHATE 2- / D-aminoacyl-tRNA deacylase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.83 Å
AuthorsLiu, Y. / Skarina, T. / Dong, A. / Kudritskam, M. / Savchenko, A. / Pai, E.F. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Conserved Hypothetical Protein AF0625
Authors: Liu, Y. / Skarina, T. / Dong, A. / Kudritskam, M. / Savchenko, A. / Pai, E.F. / Edwards, A.
History
DepositionFeb 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical UPF0204 protein AF0625
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1492
Polymers31,9731
Non-polymers1761
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.294, 73.787, 99.232
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 Hypothetical UPF0204 protein AF0625


Mass: 31973.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: gi|2649994 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Keywords: chain A / References: UniProt: O29630
#2: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.08 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: PEG3350, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 4, 2005 / Details: xenocs multilayer confocal mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.83→80 Å / Num. all: 24272 / Num. obs: 22078 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 17.4
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 3.26 / Num. unique all: 808 / Rsym value: 0.448 / % possible all: 69.5

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.83→25.04 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 542777.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: O v8.0 was also used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1058 4.8 %RANDOM
Rwork0.206 ---
obs0.206 22078 91 %-
all-24272 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.8674 Å2 / ksol: 0.37799 e/Å3
Displacement parametersBiso mean: 25.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.69 Å20 Å20 Å2
2---2.9 Å20 Å2
3---8.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.83→25.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2252 0 9 213 2474
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.112.5
LS refinement shellResolution: 1.83→1.94 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 151 5.3 %
Rwork0.355 2688 -
obs-2688 71.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4POP_XPLOR_PAR.TXTPOP_XPLOR_TOP.TXT

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