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- PDB-2eo4: Crystal structure of hypothetical histidine triad nucleotide-bind... -

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Basic information

Entry
Database: PDB / ID: 2eo4
TitleCrystal structure of hypothetical histidine triad nucleotide-binding protein ST2152 from Sulfolobus tokodaii strain7
Components150aa long hypothetical histidine triad nucleotide-binding protein
KeywordsHYDROLASE / Hit family / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


purine ribonucleotide metabolic process / adenylylsulfatase activity / sulfur compound metabolic process / metal ion binding
Similarity search - Function
HINT family / Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily ...HINT family / Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / HIT domain-containing protein
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of hypothetical histidine triad nucleotide-binding protein ST2152 from Sulfolobus tokodaii strain7
Authors: Mizutani, H. / Kunishima, N.
History
DepositionMar 29, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 150aa long hypothetical histidine triad nucleotide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4893
Polymers17,3291
Non-polymers1602
Water2,522140
1
A: 150aa long hypothetical histidine triad nucleotide-binding protein
hetero molecules

A: 150aa long hypothetical histidine triad nucleotide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9796
Polymers34,6582
Non-polymers3214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2880 Å2
ΔGint-29 kcal/mol
Surface area15360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.219, 71.219, 99.223
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 150aa long hypothetical histidine triad nucleotide-binding protein


Mass: 17328.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: strain7 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q96YM2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.63 Å3/Da / Density % sol: 66.11 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.6
Details: 0.63M NaH2PO4, 0.07M K2HPO4, pH 5.6, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 6, 2007
RadiationMonochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 24209 / Num. obs: 24209 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.06 / Net I/σ(I): 16.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 11 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 6.58 / Num. unique all: 2359 / Rsym value: 0.356 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XQU

1xqu
PDB Unreleased entry


Resolution: 1.8→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1395157.58 / 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
Rfree0.228 1214 5 %RANDOM
Rwork0.205 ---
all0.206 24163 --
obs0.205 24163 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7723 Å2 / ksol: 0.38931 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.54 Å20 Å20 Å2
2---4.54 Å20 Å2
3---9.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 6 140 1371
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.238 187 4.9 %
Rwork0.221 3657 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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