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- PDB-6bme: Crystal structure of Chlamydomonas reinhardtii THB4 -

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Basic information

Entry
Database: PDB / ID: 6bme
TitleCrystal structure of Chlamydomonas reinhardtii THB4
ComponentsTruncated hemoglobin 4
KeywordsHeme Binding Protein / globin / heme / truncated hemoglobin / 2-on-2 hemoglobin / lysine axial ligand / hexacoordinate
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 / Bacterial-like globin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Truncated hemoglobin 4
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.899 Å
AuthorsRusso, M.M. / 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: Biochim Biophys Acta Gen Subj / Year: 2018
Title: Lysine as a heme iron ligand: A property common to three truncated hemoglobins from Chlamydomonas reinhardtii.
Authors: Johnson, E.A. / Russo, M.M. / Nye, D.B. / Schlessman, J.L. / Lecomte, J.T.J.
History
DepositionNov 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 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

Downloads & links

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Assembly

Deposited unit
A: Truncated hemoglobin 4
B: Truncated hemoglobin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5116
Polymers28,0862
Non-polymers1,4254
Water3,387188
1
A: Truncated hemoglobin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7563
Polymers14,0431
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Truncated hemoglobin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7563
Polymers14,0431
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.400, 68.300, 49.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Truncated hemoglobin 4


Mass: 14043.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: THB4 / Production host: Escherichia coli (E. coli) / References: UniProt: R9RY64
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Ammonium Sulfate, 0.1 M Bis-Tris pH 5.5, 20% 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: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.899→20.68 Å / Num. obs: 38306 / % possible obs: 99.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 17.74 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 32.37
Reflection shellResolution: 1.899→1.97 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 5 / Num. unique obs: 3832 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575: ???refinement
PDB_EXTRACT3.22data extraction
CrysalisPro1.171.36.32data reduction
CrysalisPro1.171.36.32data scaling
PHENIX1.11.1_2575phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.899→20.677 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.12 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2269 3754 9.82 %
Rwork0.1876 --
obs0.1915 38227 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.66 Å2 / Biso mean: 20.4163 Å2 / Biso min: 6.49 Å2
Refinement stepCycle: final / Resolution: 1.899→20.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 96 188 2233
Biso mean--15.56 24.57 -
Num. residues----252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082105
X-RAY DIFFRACTIONf_angle_d0.7362866
X-RAY DIFFRACTIONf_chiral_restr0.045299
X-RAY DIFFRACTIONf_plane_restr0.005358
X-RAY DIFFRACTIONf_dihedral_angle_d13.3031180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8992-1.92330.28831530.23291154130797
1.9233-1.94850.32541330.219913001433100
1.9485-1.97520.28461250.218113061431100
1.9752-2.00340.25421400.226312621402100
2.0034-2.03330.23581310.19412971428100
2.0333-2.0650.27021410.194813021443100
2.065-2.09890.19691550.193612281383100
2.0989-2.1350.25381550.18512721427100
2.135-2.17380.29031260.197113151441100
2.1738-2.21560.26661350.194912761411100
2.2156-2.26070.26621490.186912631412100
2.2607-2.30980.20771340.187512741408100
2.3098-2.36350.27951200.20313221442100
2.3635-2.42250.24161580.19212401398100
2.4225-2.48790.24931390.193312981437100
2.4879-2.5610.23081400.197612951435100
2.561-2.64350.23351390.192912511390100
2.6435-2.73770.25521430.200412961439100
2.7377-2.84710.24761390.197812691408100
2.8471-2.97630.22261140.198413111425100
2.9763-3.13270.23251580.200112611419100
3.1327-3.32820.22931390.200712641403100
3.3282-3.5840.20471370.192112831420100
3.584-3.94240.16031510.154312581409100
3.9424-4.50770.16331280.153813141442100
4.5077-5.65990.17471370.167912861423100
5.6599-20.67770.2471350.171512761411100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.79310.8424-0.24651.82220.33871.7589-0.03970.1347-0.1269-0.03260.03320.04840.2672-0.1822-0.0050.1312-0.04690.0060.1038-0.01590.092630.314615.995614.6772
22.43831.1803-0.41242.0134-0.97332.50250.1077-0.23310.02470.1518-0.1539-0.0815-0.22020.18690.03110.1334-0.0598-0.01630.12180.00780.098424.645317.571839.4132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 32 through 158)A32 - 158
2X-RAY DIFFRACTION2(chain 'B' and resid 33 through 157)B33 - 157

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