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- PDB-1ixl: Crystal structure of uncharacterized protein PH1136 from Pyrococc... -

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Basic information

Entry
Database: PDB / ID: 1ixl
TitleCrystal structure of uncharacterized protein PH1136 from Pyrococcus horikoshii
Componentshypothetical protein PH1136
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha+beta / hot-dog-fold
Function / homology
Function and homology information


acyl-CoA hydrolase activity
Similarity search - Function
: / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Thioesterase domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 Å
AuthorsTajika, Y. / Sakai, N. / Tanaka, Y. / Yao, M. / Watanabe, N. / Tanaka, I.
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of conserved protein PH1136 from Pyrococcus horikoshii.
Authors: Tajika, Y. / Sakai, N. / Tanaka, Y. / Yao, M. / Watanabe, N. / Tanaka, I.
History
DepositionJun 27, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PH1136


Theoretical massNumber of molelcules
Total (without water)14,8931
Polymers14,8931
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein PH1136

A: hypothetical protein PH1136


Theoretical massNumber of molelcules
Total (without water)29,7862
Polymers29,7862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3130 Å2
ΔGint-26 kcal/mol
Surface area11780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.5, 57.5, 79.5
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein hypothetical protein PH1136


Mass: 14893.058 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET-22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O58863
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: Tris-HCl, Ammonium Sulfate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTris-HCl1droppH8.5
220 mg/mlprotein1drop
30.1 MTris-HCl1reservoirpH8.0-9.0
42.0-2.8 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 0.9000, 0.9785, 0.9791
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 4, 2002
RadiationMonochromator: MIRRORS + Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97851
30.97911
ReflectionResolution: 1.94→31 Å / Num. obs: 11527 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 8.23 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.1
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 8.39 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1174 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.332

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
WARPmodel building
CNSrefinement
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.94→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1078 9.8 %RANDOM
Rwork0.199 ---
all-11035 --
obs-11527 95 %-
Solvent computationSolvent model: throughput / Bsol: 49.8 Å2 / ksol: 0.462 e/Å3
Displacement parametersBiso mean: 30.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-1.51 Å20 Å2
2---0.55 Å20 Å2
3---1.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.288 Å-
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.94→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1027 0 0 89 1116
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.564
X-RAY DIFFRACTIONc_dihedral_angle_d26.117
X-RAY DIFFRACTIONc_improper_angle_d0.791
X-RAY DIFFRACTIONc_mcbond_it1.97
X-RAY DIFFRACTIONc_mcangle_it2.52
X-RAY DIFFRACTIONc_scbond_it3.5
X-RAY DIFFRACTIONc_scangle_it4.95
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.94-2.010.25311010.20.239970108095
2.01-2.090.2521240.214112997
2.09-2.180.2321080.219111198
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Refinement
*PLUS
Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.117
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.791

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