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- PDB-2yzq: Crystal structure of uncharacterized conserved protein from Pyroc... -

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Basic information

Entry
Database: PDB / ID: 2yzq
TitleCrystal structure of uncharacterized conserved protein from Pyrococcus horikoshii
ComponentsPutative uncharacterized protein PH1780
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / sheet/helix/sheet/sheet/helix / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / CBS domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.63 Å
AuthorsKanagawa, M. / Minami, Y. / Watanabe, N. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized conserved protein from Pyrococcus horikoshii
Authors: Kanagawa, M. / Minami, Y. / Watanabe, N. / Yokoyama, S. / Kuramitsu, S.
History
DepositionMay 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Putative uncharacterized protein PH1780
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3502
Polymers31,9521
Non-polymers3981
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative uncharacterized protein PH1780
hetero molecules

A: Putative uncharacterized protein PH1780
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7004
Polymers63,9032
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.753, 75.008, 49.661
Angle α, β, γ (deg.)90.00, 119.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-6125-

HOH

21A-6232-

HOH

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Components

#1: Protein Putative uncharacterized protein PH1780


Mass: 31951.623 Da / Num. of mol.: 1 / Fragment: residues in database 5-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: O59416
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.2M Lithium Sulfate, 30% PEG400, 0.1M Tris-HCl, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B211
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT22.29
Detector
TypeIDDetectorDate
RIGAKU JUPITER 2101CCDDec 5, 2006
RIGAKU RAXIS VII2IMAGE PLATEJan 9, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Fixed exit Si double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.291
ReflectionResolution: 1.63→50 Å / Num. obs: 73474 / % possible obs: 95.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.153 / Num. unique all: 6502 / % possible all: 84.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.63→29.96 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 206600.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.243 7165 9.9 %RANDOM
Rwork0.225 ---
obs0.225 72407 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.7468 Å2 / ksol: 0.398704 e/Å3
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.6 Å20 Å20.93 Å2
2--2.77 Å20 Å2
3----0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.63→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 27 345 2133
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.22.5
LS refinement shellResolution: 1.63→1.73 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 1020 9.5 %
Rwork0.249 9718 -
obs--83.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramsam.top
X-RAY DIFFRACTION3sam.paramwater.top

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