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- PDB-2iel: CRYSTAL STRUCTURE OF TT0030 from Thermus Thermophilus -

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Basic information

Entry
Database: PDB / ID: 2iel
TitleCRYSTAL STRUCTURE OF TT0030 from Thermus Thermophilus
ComponentsHypothetical Protein TT0030Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / TT0030 / Thermus Thermophilus / PSI / PROTEIN STRUCTURE INITIATIVE / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG
Function / homologyHUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsZhu, J. / Huang, J. / Stepanyuk, G. / Chen, L. / Chang, J. / Zhao, M. / Xu, H. / Liu, Z.J. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF TT0030 from Thermus Thermophilus AT 1.6 ANGSTROMS RESOLUTION
Authors: Zhu, J. / Huang, J. / Stepanyuk, G. / Chen, L. / Chang, J. / Zhao, M. / Xu, H. / Liu, Z.J. / Rose, J.P. / Wang, B.C.
History
DepositionSep 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 13, 2017Group: Refinement description / Category: refine / Item: _refine.pdbx_method_to_determine_struct
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical Protein TT0030
B: Hypothetical Protein TT0030


Theoretical massNumber of molelcules
Total (without water)30,1392
Polymers30,1392
Non-polymers00
Water3,117173
1
A: Hypothetical Protein TT0030
B: Hypothetical Protein TT0030

A: Hypothetical Protein TT0030
B: Hypothetical Protein TT0030

A: Hypothetical Protein TT0030
B: Hypothetical Protein TT0030

A: Hypothetical Protein TT0030
B: Hypothetical Protein TT0030


Theoretical massNumber of molelcules
Total (without water)120,5558
Polymers120,5558
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)89.584, 89.584, 66.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 5 / Auth seq-ID: 3 - 135 / Label seq-ID: 3 - 135

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsPISA SAYS THAT IS IS A A4B4 OCTOMER REPRESENTED BY A TWO LAYER TETRAMER

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Components

#1: Protein Hypothetical Protein TT0030 / Hypothesis


Mass: 15069.342 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TT0030 / Plasmid: PET16 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q72LM7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.15 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 6.9
Details: MODIFIED MICROBATCH USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (28.3 mg/ml) AND SOLUTION CONTAING 10% GLYCEROL, 1.26M TR-ISODIUM CITRATE DIHYDRATE, 0.09M ...Details: MODIFIED MICROBATCH USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (28.3 mg/ml) AND SOLUTION CONTAING 10% GLYCEROL, 1.26M TR-ISODIUM CITRATE DIHYDRATE, 0.09M HEPES pH 7.5, Temperature 291K., pH 6.9, MICROBATCH UNDER OIL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2006 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 30385 / % possible obs: 71.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 12.2 % / Rsym value: 0.045 / Net I/σ(I): 57.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.77 / Num. unique all: 1291 / Rsym value: 0.28 / % possible all: 30.6

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Processing

Software
NameVersionClassification
Sca2Structuremodel building
REFMAC5.2.0019refinement
SERGUIdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SCA2STRUCTUREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→18.59 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.969 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.139 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2791 1666 5.6 %RANDOM
Rwork0.25664 ---
all0.26794 28211 --
obs0.26794 28221 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.844 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→18.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 0 173 2168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222039
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.992781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.675254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59422.70685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26415325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2211520
X-RAY DIFFRACTIONr_chiral_restr0.0670.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021544
X-RAY DIFFRACTIONr_nbd_refined0.1830.2890
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21344
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.28
X-RAY DIFFRACTIONr_mcbond_it0.6491.51338
X-RAY DIFFRACTIONr_mcangle_it1.08522082
X-RAY DIFFRACTIONr_scbond_it1.5563790
X-RAY DIFFRACTIONr_scangle_it2.4414.5699
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
500medium positional0.130.5
463loose positional0.655
500medium thermal1.22
463loose thermal1.6510
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.576 17 -
Rwork0.443 457 -
obs-457 100 %

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