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- PDB-2cz8: Crystal Structure of tt0972 protein from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 2cz8
TitleCrystal Structure of tt0972 protein from Thermus thermophilus
Componentstt0972 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / DODECAMER / FLAVIN / flavin-adenine dinucleotide / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / Dodecin / Dodecin-like superfamily / Dodecin / Flavin-binding protein dodecin / Dodecin-like / Dodecin subunit-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / PHOSPHATE ION / : / Dodecin
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKumei, M. / Inagaki, E. / Nakano, N. / Shinkai, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of tt0972 protein from Thermus thermophilus
Authors: Kumei, M. / Inagaki, E. / Nakano, N. / Shinkai, A. / Yokoyama, S.
History
DepositionJul 11, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_alt_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.ptnr1_symmetry / _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_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: tt0972 protein
B: tt0972 protein
C: tt0972 protein
D: tt0972 protein
E: tt0972 protein
F: tt0972 protein
G: tt0972 protein
H: tt0972 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,37529
Polymers62,0798
Non-polymers7,29621
Water11,295627
1
A: tt0972 protein
B: tt0972 protein
C: tt0972 protein
D: tt0972 protein
hetero molecules

A: tt0972 protein
B: tt0972 protein
C: tt0972 protein
D: tt0972 protein
hetero molecules

A: tt0972 protein
B: tt0972 protein
C: tt0972 protein
D: tt0972 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,92042
Polymers93,11912
Non-polymers10,80130
Water21612
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 area43670 Å2
ΔGint-140 kcal/mol
Surface area30080 Å2
MethodPISA, PQS
2
E: tt0972 protein
F: tt0972 protein
G: tt0972 protein
H: tt0972 protein
hetero molecules

E: tt0972 protein
F: tt0972 protein
G: tt0972 protein
H: tt0972 protein
hetero molecules

E: tt0972 protein
F: tt0972 protein
G: tt0972 protein
H: tt0972 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,20545
Polymers93,11912
Non-polymers11,08633
Water21612
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 area44600 Å2
ΔGint-147 kcal/mol
Surface area30170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.360, 66.360, 124.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-1150-

K

21D-2102-

PO4

31E-1152-

K

41B-2181-

HOH

51B-2182-

HOH

61B-2183-

HOH

71F-2180-

HOH

81H-2187-

HOH

DetailsThe biological assembly may be a dodecamer generated from the four protomers in the asymmetric unit by the operations:1-y,x-y,z and 1-x+y,1-x,z.

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Components

#1: Protein
tt0972 protein


Mass: 7759.931 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: GenBank: 55772813, UniProt: Q5SIE3*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.6 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.8
Details: SODIUM, potassium phosphate, pH 5.8, MICRO BATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.8 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: May 17, 2005 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 96989 / Num. obs: 96989 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 24.7
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.1 / Num. unique all: 8276 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1mog

1mog


Resolution: 1.5→29.28 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 493873.29 / 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
Rfree0.229 4913 5.1 %RANDOM
Rwork0.205 ---
obs0.205 96989 98.7 %-
all-96989 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.6535 Å2 / ksol: 0.364341 e/Å3
Displacement parametersBiso mean: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20.32 Å20 Å2
2---0.16 Å20 Å2
3---0.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.5→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4256 0 473 627 5356
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.239 777 4.9 %
Rwork0.209 15094 -
obs-15871 97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4SOL.paramSOL.top

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