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- PDB-1yoy: Predicted coding region AF1432 from Archaeoglobus Fulgidus -

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Basic information

Entry
Database: PDB / ID: 1yoy
TitlePredicted coding region AF1432 from Archaeoglobus Fulgidus
Componentshypothetical protein AF1432
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / AF1432 / APC5594 / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


5'-deoxynucleotidase / 5'-deoxynucleotidase activity / metal ion binding / cytoplasm
Similarity search - Function
HD domain / 5'-deoxynucleotidase YfbR/HDDC2 / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
5'-deoxynucleotidase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMidwest Center for Structural Genomics (MCSG) / Lunin, V.V. / Savchenko, A. / Joachimiak, A.
CitationJournal: To be Published
Title: The crystal structure of predicted coding region AF1432 from Archaeoglobus Fulgidus
Authors: Lunin, V.V. / Evdokimova, E. / Kudritskaya, M. / Joachimiak, A. / Edwards, A. / Savchenko, A.
History
DepositionJan 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein AF1432


Theoretical massNumber of molelcules
Total (without water)20,0161
Polymers20,0161
Non-polymers00
Water1,42379
1
A: hypothetical protein AF1432

A: hypothetical protein AF1432


Theoretical massNumber of molelcules
Total (without water)40,0322
Polymers40,0322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5110 Å2
ΔGint-51 kcal/mol
Surface area13540 Å2
MethodPISA
2
A: hypothetical protein AF1432
x 6


Theoretical massNumber of molelcules
Total (without water)120,0966
Polymers120,0966
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area21750 Å2
ΔGint-200 kcal/mol
Surface area34190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.799, 131.799, 58.178
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe second part of the biological assembly is generated by symmetry operator (y, x, -z)

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Components

#1: Protein hypothetical protein AF1432


Mass: 20015.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Plasmid: MODIFIED PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O28840
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 2.5M (NH4)2SO4, 0.1M t-Na citrate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97945 / Wavelength: 0.97945 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 13228 / Num. obs: 13058 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.07 Å / % possible all: 65.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.46 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.496 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23589 669 5.1 %RANDOM
Rwork0.18362 ---
all0.18611 13228 --
obs0.18611 12370 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.091 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 0 79 1251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221197
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.631.9481616
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4835144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22324.10756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15815214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.554157
X-RAY DIFFRACTIONr_chiral_restr0.1120.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02892
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2515
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2829
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1851.5747
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.03321165
X-RAY DIFFRACTIONr_scbond_it3.2813524
X-RAY DIFFRACTIONr_scangle_it5.0594.5451
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 54 -
Rwork0.241 793 -
obs--100 %

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