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- PDB-1ynb: crystal structure of genomics APC5600 -

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Basic information

Entry
Database: PDB / ID: 1ynb
Titlecrystal structure of genomics APC5600
Componentshypothetical protein AF1432Hypothesis
KeywordsHYDROLASE / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Sulfur SAD
Function / homology
Function and homology information


5'-deoxynucleotidase / 5'-deoxynucleotidase activity / metal ion binding
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 / Sulfur SAD / Resolution: 1.76 Å
AuthorsDong, A. / Skarina, T. / Savchenko, A. / Pai, E.F. / Joachimiak, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of genomics AF1432 by Sulfur SAD methods
Authors: Dong, A. / Skarina, T. / Savchenko, A. / Pai, E.F. / Edwards, A.
History
DepositionJan 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 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 5, 2011Group: Structure summary
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE The authors state that electron density clearly shows that residue at position 43 is not ...SEQUENCE The authors state that electron density clearly shows that residue at position 43 is not SER. The residue is modelled as ASN because it better fits the environment. There was no mutation made for this protein.
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS NOT YET KNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein AF1432
B: hypothetical protein AF1432
C: hypothetical protein AF1432


Theoretical massNumber of molelcules
Total (without water)59,5433
Polymers59,5433
Non-polymers00
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein AF1432
B: hypothetical protein AF1432
C: hypothetical protein AF1432

A: hypothetical protein AF1432
B: hypothetical protein AF1432
C: hypothetical protein AF1432


Theoretical massNumber of molelcules
Total (without water)119,0876
Polymers119,0876
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area26750 Å2
ΔGint-231 kcal/mol
Surface area35330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.320, 131.410, 58.560
Angle α, β, γ (deg.)90.00, 117.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein hypothetical protein AF1432 / Hypothesis


Mass: 19847.797 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF1432 / Plasmid: 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 / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.46 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ammonium Sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2004
RadiationMonochromator: Si (111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 56839 / Num. obs: 55813 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 17
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.039 / Mean I/σ(I) obs: 17 / Num. unique all: 55813 / Rsym value: 0.039 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
ARP/wARPmodel building
RefinementMethod to determine structure: Sulfur SAD / Resolution: 1.76→28.36 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 535544.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1057 2 %RANDOM
Rwork0.206 ---
obs0.206 52535 92.6 %-
all-56681 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.5753 Å2 / ksol: 0.404258 e/Å3
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.07 Å20 Å22.63 Å2
2--2.91 Å20 Å2
3----5.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.76→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4023 0 0 280 4303
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 1.76→1.87 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 159 2.1 %
Rwork0.302 7317 -
obs--79.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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