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- PDB-8h17: Crystal structure of the Globin domain of Thermosynechococcus elo... -

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Basic information

Entry
Database: PDB / ID: 8h17
TitleCrystal structure of the Globin domain of Thermosynechococcus elongatus BP-1
ComponentsTlr1989 protein
KeywordsOXYGEN BINDING / Thermosynechococcus vestitus BP-1 / Haemoglobin / Imidazole / Penta-cordinated heme / Heme binding / Iron / Thermophile / Cyanobacteria / Synechococcus
Function / homology
Function and homology information


oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin-sensor domain / Protoglobin / Globin/Protoglobin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Tlr1989 protein
Similarity search - Component
Biological speciesThermosynechococcus vestitus BP-1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMathur, S. / Yadav, S.K. / Pal, K.R. / Kundu, S.
Funding support India, 5items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
Department of Science & Technology (DST, India) India
Delhi University, IoE India
Defense research development organization India
University Grants Commission India
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: A novel single sensor hemoglobin domain from the thermophilic cyanobacteria Thermosynechococcus elongatus BP-1 exhibits higher pH but lower thermal stability compared to globins from mesophilic organisms.
Authors: Mathur, S. / Yadav, S.K. / Yadav, K. / Bhatt, S. / Kundu, S.
History
DepositionSep 30, 2022Deposition site: PDBJ / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tlr1989 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5303
Polymers22,8441
Non-polymers6862
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-17 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.041, 54.041, 112.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Tlr1989 protein


Mass: 22844.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vestitus BP-1 (bacteria)
Gene: tlr1989 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8DHH0
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.87 Å3/Da / Density % sol: 35 % / Description: Red colour, Thick square plate
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.5 M Ammonium sulfate, 0.1 M MES 0.02 M Cobalt chloride hexahydrate 10% Glycerol
PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.15→35 Å / Num. obs: 9714 / % possible obs: 99.7 % / Redundancy: 23.9 % / CC1/2: 0.99 / Net I/σ(I): 65.5
Reflection shellResolution: 2.15→2.23 Å / Num. unique obs: 932 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alfa fold

Resolution: 2.15→22.23 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.457 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22292 461 4.8 %RANDOM
Rwork0.1762 ---
obs0.17855 9193 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.414 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2---1.28 Å20 Å2
3---2.56 Å2
Refinement stepCycle: 1 / Resolution: 2.15→22.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1251 0 48 25 1324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0121324
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161196
X-RAY DIFFRACTIONr_angle_refined_deg1.8741.6921802
X-RAY DIFFRACTIONr_angle_other_deg1.0671.5882762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0595154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.6631010
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15610217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021523
X-RAY DIFFRACTIONr_gen_planes_other0.030.02291
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7744.977622
X-RAY DIFFRACTIONr_mcbond_other2.7734.977622
X-RAY DIFFRACTIONr_mcangle_it3.9977.427774
X-RAY DIFFRACTIONr_mcangle_other3.9957.437775
X-RAY DIFFRACTIONr_scbond_it3.6285.346702
X-RAY DIFFRACTIONr_scbond_other3.6225.345700
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6157.8551028
X-RAY DIFFRACTIONr_long_range_B_refined7.37365.7691633
X-RAY DIFFRACTIONr_long_range_B_other7.37565.7331631
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.203 Å
RfactorNum. reflection% reflection
Rfree0.238 27 -
Rwork0.221 655 -
obs--98.55 %
Refinement TLS params.Method: refined / Origin x: 1.3188 Å / Origin y: -2.1972 Å / Origin z: 17.6575 Å
111213212223313233
T0.0611 Å20.007 Å2-0.0008 Å2-0.1022 Å20.0047 Å2--0.0086 Å2
L1.1733 °20.1734 °2-0.1155 °2-0.8271 °20.3465 °2--0.3753 °2
S-0.0551 Å °0.2141 Å °-0.0417 Å °-0.1019 Å °0.0701 Å °-0.0241 Å °-0.1088 Å °-0.0586 Å °-0.015 Å °

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