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- PDB-2z0r: Crystal structure of hypothetical protein TTHA0547 -

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Basic information

Entry
Database: PDB / ID: 2z0r
TitleCrystal structure of hypothetical protein TTHA0547
ComponentsPutative uncharacterized protein TTHA0547
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha/beta protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyUncharacterised protein PF11572, DUF3234 / Protein of unknown function DUF3234 / Protein of unknown function (DUF3234) / Trna Endonuclease; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / DUF3234 domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: Crystal structure of hypothetical protein TTHA0547
Authors: Murayama, K. / Kato-Murayama, M. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 9, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Putative uncharacterized protein TTHA0547
B: Putative uncharacterized protein TTHA0547
C: Putative uncharacterized protein TTHA0547
D: Putative uncharacterized protein TTHA0547
E: Putative uncharacterized protein TTHA0547
F: Putative uncharacterized protein TTHA0547
G: Putative uncharacterized protein TTHA0547
H: Putative uncharacterized protein TTHA0547
I: Putative uncharacterized protein TTHA0547
J: Putative uncharacterized protein TTHA0547
K: Putative uncharacterized protein TTHA0547
L: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,64031
Polymers140,48212
Non-polymers1,15819
Water5,152286
1
A: Putative uncharacterized protein TTHA0547
B: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5454
Polymers23,4142
Non-polymers1322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
MethodPISA
2
C: Putative uncharacterized protein TTHA0547
D: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5815
Polymers23,4142
Non-polymers1673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
MethodPISA
3
E: Putative uncharacterized protein TTHA0547
F: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7127
Polymers23,4142
Non-polymers2985
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
MethodPISA
4
G: Putative uncharacterized protein TTHA0547
H: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5815
Polymers23,4142
Non-polymers1673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
MethodPISA
5
I: Putative uncharacterized protein TTHA0547
J: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5454
Polymers23,4142
Non-polymers1322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
MethodPISA
6
K: Putative uncharacterized protein TTHA0547
L: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6776
Polymers23,4142
Non-polymers2634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
MethodPISA
7
A: Putative uncharacterized protein TTHA0547
B: Putative uncharacterized protein TTHA0547
C: Putative uncharacterized protein TTHA0547
D: Putative uncharacterized protein TTHA0547
E: Putative uncharacterized protein TTHA0547
F: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,83816
Polymers70,2416
Non-polymers59710
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
MethodPISA
8
G: Putative uncharacterized protein TTHA0547
H: Putative uncharacterized protein TTHA0547
I: Putative uncharacterized protein TTHA0547
J: Putative uncharacterized protein TTHA0547
K: Putative uncharacterized protein TTHA0547
L: Putative uncharacterized protein TTHA0547
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,80215
Polymers70,2416
Non-polymers5629
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.501, 94.297, 101.734
Angle α, β, γ (deg.)90.00, 96.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative uncharacterized protein TTHA0547


Mass: 11706.802 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKU6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.45M Ammonium sulfate, HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.97906, 0.97943, 0.964
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979061
20.979431
30.9641
ReflectionResolution: 2.3→42.84 Å / Num. obs: 56109 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Redundancy: 5 % / Biso Wilson estimate: 26.6 Å2 / Rsym value: 0.082 / Net I/σ(I): 15.8
Reflection shellResolution: 2.3→2.38 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→42.84 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1572254.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2837 5.1 %RANDOM
Rwork0.229 ---
obs0.229 56087 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.1099 Å2 / ksol: 0.359003 e/Å3
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.02 Å20 Å2-10.95 Å2
2---9.94 Å20 Å2
3---2.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9303 0 51 286 9640
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_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.442.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 500 5.5 %
Rwork0.294 8606 -
obs--97.5 %
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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