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- PDB-2d16: Crystal Structure of PH1918 protein from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2d16
TitleCrystal Structure of PH1918 protein from Pyrococcus horikoshii OT3
Componentshypothetical protein PH1918
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyTa1353-like / Adenosine specific kinase / Ta1353-like superfamily / Adenosine specific kinase / hypothetical protein tt1634 / 3-Layer(aba) Sandwich / Alpha Beta / Adenosine monophosphate-protein transferase
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLokanath, N.K. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of PH1918 protein from Pyrococcus horikoshii OT3
Authors: Lokanath, N.K. / Kunishima, N.
History
DepositionAug 14, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2006Provider: 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 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein PH1918
B: hypothetical protein PH1918
C: hypothetical protein PH1918
D: hypothetical protein PH1918
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,11012
Polymers70,6504
Non-polymers4608
Water10,737596
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: hypothetical protein PH1918
D: hypothetical protein PH1918
hetero molecules

C: hypothetical protein PH1918
D: hypothetical protein PH1918
hetero molecules

C: hypothetical protein PH1918
D: hypothetical protein PH1918
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,66518
Polymers105,9756
Non-polymers69112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area30390 Å2
ΔGint-141 kcal/mol
Surface area30420 Å2
MethodPISA, PQS
3
A: hypothetical protein PH1918
B: hypothetical protein PH1918
hetero molecules

A: hypothetical protein PH1918
B: hypothetical protein PH1918
hetero molecules

A: hypothetical protein PH1918
B: hypothetical protein PH1918
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,66518
Polymers105,9756
Non-polymers69112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.120, 66.120, 125.072
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-1001-

NA

21B-1002-

NA

31C-1003-

NA

41D-1004-

NA

51A-1102-

HOH

61A-1149-

HOH

71B-1144-

HOH

81B-1145-

HOH

91C-1054-

HOH

101C-1059-

HOH

111C-1163-

HOH

121C-1165-

HOH

131D-1137-

HOH

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Components

#1: Protein
hypothetical protein PH1918


Mass: 17662.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21-CodonPlus (DE3)-RIL / References: UniProt: O59581
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.3 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.3
Details: MES-NaOH, PEG 4000, pH 6.3, microbatch, temperature 295.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 20, 2005 / Details: Graphite
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. all: 73383 / Num. obs: 73383 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.1
Reflection shellResolution: 1.65→1.71 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VGG

1vgg


Resolution: 1.65→33.7 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1827339.78 / 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
Rfree0.204 3748 5.1 %RANDOM
Rwork0.185 ---
obs0.185 73383 100 %-
all-73383 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.7303 Å2 / ksol: 0.344327 e/Å3
Displacement parametersBiso mean: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.85 Å23.62 Å20 Å2
2--5.85 Å20 Å2
3----11.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.65→33.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4948 0 28 596 5572
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_mcangle_it1.372
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 613 5.1 %
Rwork0.281 11409 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4gol.paramgol.top

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