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- PDB-2dcl: Structure of PH1503 protein from Pyrococcus Horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2dcl
TitleStructure of PH1503 protein from Pyrococcus Horikoshii OT3
ComponentsHypothetical UPF0166 protein PH1503
KeywordsStructural genomics / unknown function / Hexamer / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


UPF0166 / Uncharacterized ACR, COG1993 / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / UPF0166 protein PH1503
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsBagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of PH1503 protein from Pyrococcus Horikoshii OT3
Authors: Bagautdinov, B. / Kunishima, N.
History
DepositionJan 8, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 25, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value ..._reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value
Revision 1.4Oct 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical UPF0166 protein PH1503
B: Hypothetical UPF0166 protein PH1503
C: Hypothetical UPF0166 protein PH1503
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0046
Polymers43,9623
Non-polymers1,0423
Water2,216123
1
A: Hypothetical UPF0166 protein PH1503
B: Hypothetical UPF0166 protein PH1503
C: Hypothetical UPF0166 protein PH1503
hetero molecules

A: Hypothetical UPF0166 protein PH1503
B: Hypothetical UPF0166 protein PH1503
C: Hypothetical UPF0166 protein PH1503
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,00712
Polymers87,9246
Non-polymers2,0836
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area21160 Å2
ΔGint-110 kcal/mol
Surface area24350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)107.562, 59.647, 66.738
Angle α, β, γ (deg.)90.00, 122.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-907-

HOH

21A-924-

HOH

31A-931-

HOH

41B-911-

HOH

51C-141-

HOH

DetailsThe biological assembly is a hexamer.

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Components

#1: Protein Hypothetical UPF0166 protein PH1503


Mass: 14654.028 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1503 / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O59172
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.5
Details: 20% PEG 3000, 100mM Acetate, pH 4.5, microbatch, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 22, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. all: 16269 / Num. obs: 15774 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 43.7 Å2 / Net I/σ(I): 16.5
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1550 / % possible all: 83.9

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O51

1o51


Resolution: 2.28→32.82 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 790 -RANDOM
Rwork0.244 ---
obs0.244 15772 96.2 %-
all-16269 --
Displacement parametersBiso mean: 60.19 Å2
Baniso -1Baniso -2Baniso -3
1-8.23 Å20 Å22.19 Å2
2--9.77 Å20 Å2
3----18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.28→32.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 69 123 2562
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.96

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