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- PDB-2zdj: Crystal Structure of TTMA177, a Hypothetical Protein from Thermus... -

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Basic information

Entry
Database: PDB / ID: 2zdj
TitleCrystal Structure of TTMA177, a Hypothetical Protein from Thermus thermophilus phage TMA
Componentshypothetical protein TTMA177
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Alpha and beta proteins (a+b) / Cystatin-like / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyNuclear Transport Factor 2; Chain: A, - #450 / : / : / Domain of unknown function (DUF6839) / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Hypothetical protein TTMA177
Function and homology information
Biological speciesThermus thermophilus phage TMA (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsAgari, Y. / Tamakoshi, M. / Yamagishi, A. / Shinkai, A. / Ebihara, A. / Yokoyama, S. / Kuramitsu, S. / Oshima, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of TTMA177, a Hypothetical Protein from Thermus thermophilus phage TMA
Authors: Agari, Y. / Tamakoshi, M. / Yamagishi, A. / Shinkai, A. / Ebihara, A. / Yokoyama, S. / Kuramitsu, S. / Oshima, T.
History
DepositionNov 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein TTMA177
B: hypothetical protein TTMA177
C: hypothetical protein TTMA177
D: hypothetical protein TTMA177


Theoretical massNumber of molelcules
Total (without water)32,7324
Polymers32,7324
Non-polymers00
Water1,964109
1
A: hypothetical protein TTMA177


Theoretical massNumber of molelcules
Total (without water)8,1831
Polymers8,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein TTMA177


Theoretical massNumber of molelcules
Total (without water)8,1831
Polymers8,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: hypothetical protein TTMA177


Theoretical massNumber of molelcules
Total (without water)8,1831
Polymers8,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: hypothetical protein TTMA177


Theoretical massNumber of molelcules
Total (without water)8,1831
Polymers8,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.421, 63.716, 71.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
hypothetical protein TTMA177


Mass: 8182.890 Da / Num. of mol.: 4 / Fragment: Residues 1-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus phage TMA (others)
Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: D0VWQ2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING.

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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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% (w/v) PEG 8000, 75mM MES, 150mM Calcium Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97893 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 22, 2007
Details: A fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror which is coated in rhodium.
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 15444 / Num. obs: 15444 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 31.44
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 8.125 / Num. unique all: 1508 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→31.86 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1546098.55 / 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
Rfree0.263 1553 10.1 %RANDOM
Rwork0.21 ---
all0.215 15329 --
obs0.21 15329 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.7484 Å2 / ksol: 0.374087 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.37 Å20 Å20 Å2
2---0.43 Å20 Å2
3----3.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.2→31.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2284 0 0 109 2393
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 251 10.1 %
Rwork0.226 2246 -
obs-2497 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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