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- PDB-6cii: Crystal structure of Chlamydomonas reinhardtii THB1 in the cyanom... -

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Basic information

Entry
Database: PDB / ID: 6cii
TitleCrystal structure of Chlamydomonas reinhardtii THB1 in the cyanomet state
ComponentsChlamydomonas reinhardtii THB1
Keywordsheme-binding protein / heme / globin / truncated hemoglobin / 2-on-2 hemoglobin / cyanide / cyanomet
Function / homology
Function and homology information


thioredoxin peroxidase activity / cell redox homeostasis / oxygen binding / cellular response to oxidative stress / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Truncated hemoglobin, group 1 / Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Putative truncated hemoglobin
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.7 Å
AuthorsMartinez, J.E. / Schlessman, J.L. / Lecomte, J.T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1330488 United States
CitationJournal: J.Inorg.Biochem. / Year: 2021
Title: Control of distal lysine coordination in a monomeric hemoglobin: A role for heme peripheral interactions
Authors: Martinez, J.E. / Schlessman, J.L. / Lecomte, J.T.J.
History
DepositionFeb 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 28, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chlamydomonas reinhardtii THB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2263
Polymers14,5831
Non-polymers6432
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.992, 45.992, 121.277
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

21A-405-

HOH

31A-428-

HOH

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Components

#1: Protein Chlamydomonas reinhardtii THB1 / Truncated hemoglobin 1


Mass: 14583.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: THB1, CHLREDRAFT_81856 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8JAR4
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Bis-Tris pH 5.5, 30% PEG 3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→21.502 Å / Num. obs: 27344 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 14.96 Å2 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.013 / Rrim(I) all: 0.044 / Net I/σ(I): 36.06
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 5.88 / Num. unique obs: 2732 / Rpim(I) all: 0.093 / Rrim(I) all: 0.214 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13rc1_2954: ???)refinement
CrysalisPro1.171.36.32data reduction
CrysalisPro1.171.36.32data scaling
PHENIX1.13rc1_2954phasing
Coot0.8.8model building
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.7→21.502 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.98
RfactorNum. reflection% reflection
Rfree0.1905 2722 9.95 %
Rwork0.1632 --
obs0.166 27344 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.47 Å2 / Biso mean: 18.1763 Å2 / Biso min: 5.65 Å2
Refinement stepCycle: final / Resolution: 1.7→21.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms959 0 45 140 1144
Biso mean--14.15 27.52 -
Num. residues----124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011083
X-RAY DIFFRACTIONf_angle_d1.1031482
X-RAY DIFFRACTIONf_dihedral_angle_d15.572407
X-RAY DIFFRACTIONf_chiral_restr0.057149
X-RAY DIFFRACTIONf_plane_restr0.006194
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.73090.26821420.191712871429
1.7309-1.76420.19961460.177613011447
1.7642-1.80020.22531410.165312951436
1.8002-1.83930.20591430.155713061449
1.8393-1.88210.22361430.155112721415
1.8821-1.92910.18131420.170413081450
1.9291-1.98120.2121390.159812981437
1.9812-2.03950.2381430.172413001443
2.0395-2.10530.24621480.16812931441
2.1053-2.18040.20951470.169713121459
2.1804-2.26760.18791420.157912591401
2.2676-2.37070.2171460.159913121458
2.3707-2.49550.18091410.159612921433
2.4955-2.65160.19531460.158513011447
2.6516-2.85590.18111450.173112981443
2.8559-3.14250.19111460.163912811427
3.1425-3.59540.16961390.160812971436
3.5954-4.52290.15591410.142713041445
4.5229-21.50350.16371420.176113061448

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