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- PDB-1tua: 1.5 A Crystal Structure of a Protein of Unknown Function APE0754 ... -

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Basic information

Entry
Database: PDB / ID: 1tua
Title1.5 A Crystal Structure of a Protein of Unknown Function APE0754 from Aeropyrum pernix
ComponentsHypothetical protein APE0754
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein structure initiative / MCSG / Aeropyrum pernix / Four layers alpha-beta sandwich / PSI / Midwest Center for Structural Genomics
Function / homology
Function and homology information


KH domain protein, archaea / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
K Homology domain-containing protein
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsZhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.5A crystal structure of a hypothetical protein APE0754 from Aeropyrum pernix
Authors: Zhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJun 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: 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
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 APE0754


Theoretical massNumber of molelcules
Total (without water)21,7711
Polymers21,7711
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.710, 28.987, 69.924
Angle α, β, γ (deg.)90.00, 95.85, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis protein existed as monomer. The deposited coords. represents the monomer in the asymmtric unit

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Components

#1: Protein Hypothetical protein APE0754


Mass: 21770.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: GI:14600942 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9YE16
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.412 Å3/Da / Density % sol: 47 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9797 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jun 21, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 63292 / Num. obs: 61520 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 1.9 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.61
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.15 / Num. unique all: 6292 / % possible all: 95.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→20.88 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 439793.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2879 4.9 %RANDOM
Rwork0.208 ---
all0.21 63292 --
obs0.208 58656 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.2203 Å2 / ksol: 0.443564 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å2-0.8 Å2
2--1.17 Å20 Å2
3----0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.5→20.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 0 164 1667
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 419 4.9 %
Rwork0.285 8210 -
obs--81.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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