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- PDB-3ayv: TTHB071 protein from Thermus thermophilus HB8 soaking with ZnCl2 -

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Basic information

Entry
Database: PDB / ID: 3ayv
TitleTTHB071 protein from Thermus thermophilus HB8 soaking with ZnCl2
ComponentsPutative uncharacterized protein TTHB071
KeywordsUNKNOWN FUNCTION / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Tim Barrel
Function / homology
Function and homology information


phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / DNA binding / zinc ion binding
Similarity search - Function
AP endonuclease 2 / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Xylose isomerase-like TIM barrel domain-containing protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsNakane, S. / Wakamatsu, T. / Fukui, K. / Nakagawa, N. / Masui, R. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: In vivo, in vitro, and x-ray crystallographic analyses suggest the involvement of an uncharacterized triose-phosphate isomerase (TIM) barrel protein in protection against oxidative stress
Authors: Nakane, S. / Wakamatsu, T. / Masui, R. / Kuramitsu, S. / Fukui, K.
History
DepositionMay 17, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Mar 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_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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_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_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.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_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: Putative uncharacterized protein TTHB071
B: Putative uncharacterized protein TTHB071
C: Putative uncharacterized protein TTHB071
D: Putative uncharacterized protein TTHB071
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,96216
Polymers113,1774
Non-polymers78512
Water14,034779
1
A: Putative uncharacterized protein TTHB071
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4914
Polymers28,2941
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative uncharacterized protein TTHB071
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4914
Polymers28,2941
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative uncharacterized protein TTHB071
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4914
Polymers28,2941
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative uncharacterized protein TTHB071
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4914
Polymers28,2941
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Putative uncharacterized protein TTHB071
D: Putative uncharacterized protein TTHB071
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9818
Polymers56,5892
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-10 kcal/mol
Surface area19790 Å2
MethodPISA
6
B: Putative uncharacterized protein TTHB071
C: Putative uncharacterized protein TTHB071
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9818
Polymers56,5892
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-9 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.085, 93.375, 87.379
Angle α, β, γ (deg.)90.000, 95.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative uncharacterized protein TTHB071


Mass: 28294.357 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHB071 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q53W91
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 0.05M Mg Chloride, 30%(v/v) PEG MME 550, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1.282186 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2011
Diffraction measurementDetails: 1.00 degrees, 4.7 sec, detector distance 130.00 mm / Method: \w scans
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282186 Å / Relative weight: 1
ReflectionAv R equivalents: 0.055 / Number: 1347990
ReflectionResolution: 1.85→50 Å / Num. all: 1347990 / Num. obs: 1347990 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.8 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 49.414
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 11.806 / Rsym value: 0.253 / % possible all: 98.9
Cell measurementReflection used: 1347990

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.34 / FOM acentric: 0.34 / FOM centric: 0.33 / Reflection: 18966 / Reflection acentric: 18099 / Reflection centric: 867
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
3.1-3.30.130.130.113336323898
3.3-3.90.270.270.2657285534194
3.9-4.40.440.440.4232153083132
4.4-5.60.440.450.3132403079161
5.6-8.90.420.430.3625932418175

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RESOLVE2.15phasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.365 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 4559 5 %RANDOM
Rwork0.172 ---
obs0.1737 90916 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.35 Å2 / Biso mean: 20.3554 Å2 / Biso min: 6.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å2-0.15 Å2
2---0.86 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7617 0 12 779 8408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217813
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.98210632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5485965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75621.728382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.182151219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.17415102
X-RAY DIFFRACTIONr_chiral_restr0.0970.21160
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216130
X-RAY DIFFRACTIONr_mcbond_it0.7711.54835
X-RAY DIFFRACTIONr_mcangle_it1.41927691
X-RAY DIFFRACTIONr_scbond_it2.44932978
X-RAY DIFFRACTIONr_scangle_it4.1024.52941
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8980.2473150.1896274674997.629
1.898-1.950.2133450.1826118654298.792
1.95-2.0060.2393380.1775974638298.903
2.006-2.0680.2222740.1765859617499.336
2.068-2.1360.2232990.1725707603799.487
2.136-2.2110.2052990.1755475579899.586
2.211-2.2940.2092800.175314561099.715
2.294-2.3870.2172700.1685141541799.889
2.387-2.4930.2052450.1734943519199.942
2.493-2.6150.2022550.1764702495899.98
2.615-2.7560.2322360.1724452469299.915
2.756-2.9220.2262240.1864273450199.911
2.922-3.1230.2021950.1913992418899.976
3.123-3.3720.22040.18437213925100
3.372-3.6920.1851880.1663405359499.972
3.692-4.1250.1851570.163125328599.909
4.125-4.7580.1611530.14127212874100
4.758-5.8150.2171230.1692347247299.919
5.815-8.1680.2211070.18118041911100
8.168-500.149520.1611010110895.848

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