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- PDB-2e67: Crystal structure of the hypothetical protein TTHB029 from Thermu... -

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Basic information

Entry
Database: PDB / ID: 2.0E+67
TitleCrystal structure of the hypothetical protein TTHB029 from Thermus thermophilus HB8
ComponentsHypothetical protein TTHB029Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / hydrolase activity / carbohydrate metabolic process / magnesium ion binding
Similarity search - Function
Carbohydrate deacetylase YdjC-like / YdjC-like protein / Glycoside hydrolase/deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Carbohydrate deacetylase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsImagawa, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Crystal structure of the YdjC-family protein TTHB029 from Thermus thermophilus HB8: structural relationship with peptidoglycan N-acetylglucosamine deacetylase.
Authors: Imagawa, T. / Iino, H. / Kanagawa, M. / Ebihara, A. / Kuramitsu, S. / Tsuge, H.
History
DepositionDec 26, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_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 TTHB029
B: Hypothetical protein TTHB029
C: Hypothetical protein TTHB029
D: Hypothetical protein TTHB029
E: Hypothetical protein TTHB029
F: Hypothetical protein TTHB029
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,95512
Polymers177,8096
Non-polymers1466
Water2,378132
1
A: Hypothetical protein TTHB029
B: Hypothetical protein TTHB029
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3184
Polymers59,2702
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Hypothetical protein TTHB029
E: Hypothetical protein TTHB029
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3184
Polymers59,2702
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Hypothetical protein TTHB029
F: Hypothetical protein TTHB029
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3184
Polymers59,2702
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)202.006, 202.006, 345.294
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

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Components

#1: Protein
Hypothetical protein TTHB029 / Hypothesis


Mass: 29634.873 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q53WD3
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20mM Na Acetate buffer, 300mM Mg Formate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B210.9
SYNCHROTRONSPring-8 BL26B220.900, 0.97919, 0.97949
Detector
TypeIDDetectorDate
RIGAKU JUPITER 2101CCDNov 5, 2004
RIGAKU JUPITER 2102CCDNov 5, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.979191
30.979491
ReflectionResolution: 2.9→50 Å / Num. obs: 56883 / % possible obs: 100 % / Observed criterion σ(F): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.354 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.885 / SU B: 12.425 / SU ML: 0.235 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / ESU R: 0.926 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25934 3026 5.1 %RANDOM
Rwork0.21904 ---
obs0.22109 56883 100 %-
all-59909 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.772 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.12 Å20 Å2
2--0.23 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12540 0 6 132 12678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02212936
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.99217688
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.63151572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46222.3600
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.04151962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.87215126
X-RAY DIFFRACTIONr_chiral_restr0.1270.21902
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210176
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.26401
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3320.28641
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2455
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0580.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.2121
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9031.58045
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.591212738
X-RAY DIFFRACTIONr_scbond_it2.40435464
X-RAY DIFFRACTIONr_scangle_it4.2734.54950
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 228 -
Rwork0.392 4100 -
obs--100 %

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