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- PDB-1wwz: Crystal structure of PH1933 from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 1wwz
TitleCrystal structure of PH1933 from Pyrococcus horikoshii OT3
Componentshypothetical protein PH1933Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pyrococcus horikoshii OT3 / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


N-acetyltransferase activity
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsAsada, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of PH1933 from Pyrococcus horikoshii OT3
Authors: Asada, Y. / Kunishima, N.
History
DepositionJan 19, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: hypothetical protein PH1933
B: hypothetical protein PH1933
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6084
Polymers36,9892
Non-polymers1,6192
Water6,738374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.504, 56.026, 125.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is dimer

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Components

#1: Protein hypothetical protein PH1933 / Hypothesis


Mass: 18494.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O59596
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5
Details: HEPES-Na, iso-Propanol, PEG 4000, Glycerol, Acetyl-CoA, pH 7.5, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1.0, 0.97907
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 11, 2004 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979071
ReflectionResolution: 1.75→30 Å / Num. all: 38152 / Num. obs: 38152 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 21.745 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.075 / Net I/σ(I): 10
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 4.11 / Num. unique all: 3724 / Rsym value: 0.378 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.75→28.28 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1879 -RANDOM
Rwork0.212 ---
all0.213 38089 --
obs0.213 38089 99.7 %-
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.25 Å20 Å20 Å2
2--6.11 Å20 Å2
3----0.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.75→28.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2573 0 102 374 3049
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.63
LS refinement shellResolution: 1.75→1.83 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.266 223 -
Rwork0.259 --
obs--97.8 %

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