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- PDB-2z07: Crystal structure of uncharacterized conserved protein from Therm... -

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Basic information

Entry
Database: PDB / ID: 2z07
TitleCrystal structure of uncharacterized conserved protein from Thermus thermophilus HB8
ComponentsPutative uncharacterized protein TTHA0978
KeywordsHYDROLASE / uncharacterized conserved protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Glc3Man9GlcNAc2 oligosaccharide glucosidase activity / oligosaccharide metabolic process / protein N-linked glycosylation
Similarity search - Function
Trehalase / : / Mannosylglycerate hydrolase MGH1-like glycoside hydrolase domain / Glycoside hydrolase family 63 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Mannosylglycerate hydrolase MGH1-like glycoside hydrolase domain-containing protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsIino, H. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized conserved protein from Thermus thermophilus HB8
Authors: Iino, H. / Yokoyama, S. / Kuramitsu, S.
History
DepositionMay 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein TTHA0978
B: Putative uncharacterized protein TTHA0978


Theoretical massNumber of molelcules
Total (without water)98,1472
Polymers98,1472
Non-polymers00
Water6,071337
1
A: Putative uncharacterized protein TTHA0978


Theoretical massNumber of molelcules
Total (without water)49,0741
Polymers49,0741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein TTHA0978


Theoretical massNumber of molelcules
Total (without water)49,0741
Polymers49,0741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Putative uncharacterized protein TTHA0978

A: Putative uncharacterized protein TTHA0978

A: Putative uncharacterized protein TTHA0978


Theoretical massNumber of molelcules
Total (without water)147,2213
Polymers147,2213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6830 Å2
MethodPISA
4
B: Putative uncharacterized protein TTHA0978

B: Putative uncharacterized protein TTHA0978

B: Putative uncharacterized protein TTHA0978


Theoretical massNumber of molelcules
Total (without water)147,2213
Polymers147,2213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.437, 93.437, 254.918
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Putative uncharacterized protein TTHA0978


Mass: 49073.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta834(DE3) / References: UniProt: Q5SJN0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 29% v/v MPD, 0.1M Sodium citrate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9789, 0.9000, 0.9794
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 9, 2005
RadiationMonochromator: SI Double-Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.91
30.97941
ReflectionResolution: 2.1→30 Å / % possible obs: 99.8 % / Redundancy: 2.8 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.39 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→19.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3849808.26 / 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
Rfree0.233 4869 10.1 %RANDOM
Rwork0.189 ---
obs0.189 48254 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.8485 Å2 / ksol: 0.374754 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å21.62 Å20 Å2
2---0.55 Å20 Å2
3---1.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6411 0 0 337 6748
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.852.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 797 9.9 %
Rwork0.212 7240 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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