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- PDB-5ytq: Crystal Structure of TTHA0139 L34A with Lanthanum from Thermus th... -

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Basic information

Entry
Database: PDB / ID: 5ytq
TitleCrystal Structure of TTHA0139 L34A with Lanthanum from Thermus thermophilus HB8
ComponentsTTHA0139
KeywordsDNA BINDING PROTEIN / RHH superfamily / DNA binding / protein phosphorylation
Function / homologyLANTHANUM (III) ION / Transcriptional regulator
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.393 Å
AuthorsTakao, K. / Inoue, M. / Fukui, K. / Yano, T. / Masui, R.
CitationJournal: To Be Published
Title: Crystal Structure of TTHA0139 L34A with Lanthanum from Thermus thermophilus HB8
Authors: Takao, K. / Inoue, M. / Fukui, K. / Yano, T. / Masui, R.
History
DepositionNov 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TTHA0139
B: TTHA0139
C: TTHA0139
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6808
Polymers25,9863
Non-polymers6955
Water63135
1
A: TTHA0139
B: TTHA0139
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7415
Polymers17,3242
Non-polymers4173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-52 kcal/mol
Surface area8200 Å2
MethodPISA
2
C: TTHA0139
hetero molecules

C: TTHA0139
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8796
Polymers17,3242
Non-polymers5564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+y+1,y,-z+1/31
Buried area5270 Å2
ΔGint-52 kcal/mol
Surface area7880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.224, 50.224, 174.648
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein TTHA0139


Mass: 8661.925 Da / Num. of mol.: 3 / Mutation: L34A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0139 / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q5SM04
#2: Chemical
ChemComp-LA / LANTHANUM (III) ION


Mass: 138.905 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: La
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 11.4mg/mL, 3.2M Sodium chloride, 0.1M Sodium acetate trihydrate, 4% 2,5 Hexanediol, 10mM Lanthanum nitrate hexahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 10313 / % possible obs: 99.8 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.031 / Net I/σ(I): 43.3
Reflection shellResolution: 2.39→2.43 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.255 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 470 / CC1/2: 0.953 / Rpim(I) all: 0.395 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.393→34.844 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.5
RfactorNum. reflection% reflection
Rfree0.2737 565 5.51 %
Rwork0.2631 --
obs0.2637 10253 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.393→34.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 5 35 1586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021553
X-RAY DIFFRACTIONf_angle_d0.4152087
X-RAY DIFFRACTIONf_dihedral_angle_d17.9561001
X-RAY DIFFRACTIONf_chiral_restr0.037257
X-RAY DIFFRACTIONf_plane_restr0.003268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3928-2.63350.39231150.33162419X-RAY DIFFRACTION100
2.6335-3.01440.33131460.3492375X-RAY DIFFRACTION100
3.0144-3.79710.34141530.30112412X-RAY DIFFRACTION99
3.7971-34.84770.21831510.2252482X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 1.3952 Å / Origin y: 31.5475 Å / Origin z: 14.5139 Å
111213212223313233
T0.5481 Å20.0697 Å20.0383 Å2-0.4582 Å2-0.1073 Å2--0.3947 Å2
L1.0354 °2-0.5827 °21.3599 °2-0.4062 °2-0.9626 °2--2.5927 °2
S0.0092 Å °-0.0269 Å °0.1796 Å °0.2098 Å °-0.1317 Å °-0.0584 Å °-0.0801 Å °-0.1315 Å °0.0988 Å °
Refinement TLS groupSelection details: all

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