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- PDB-4xdi: Structure of Chlamydomonas reinhardtii THB1 -

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Basic information

Entry
Database: PDB / ID: 4xdi
TitleStructure of Chlamydomonas reinhardtii THB1
ComponentsChlamydomonas reinhardtii THB1
KeywordsHeme Binding Protein / Group 1 truncated hemoglobin / TrHbN / TrHb1
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
PROTOPORPHYRIN IX CONTAINING FE / Putative truncated hemoglobin
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.893 Å
AuthorsRice, S.L. / Boucher, L.E. / Schlessman, J.L. / Bosch, J. / Lecomte, J.T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1330488 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of Chlamydomonas reinhardtii THB1, a group 1 truncated hemoglobin with a rare histidine-lysine heme ligation.
Authors: Rice, S.L. / Boucher, L.E. / Schlessman, J.L. / Preimesberger, M.R. / Bosch, J. / Lecomte, J.T.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Jul 20, 2016Group: Data collection
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 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: Chlamydomonas reinhardtii THB1
B: Chlamydomonas reinhardtii THB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4004
Polymers29,1672
Non-polymers1,2332
Water3,765209
1
A: Chlamydomonas reinhardtii THB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2002
Polymers14,5831
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chlamydomonas reinhardtii THB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2002
Polymers14,5831
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.513, 144.513, 79.913
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-314-

HOH

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Components

#1: Protein Chlamydomonas reinhardtii THB1 / Putative truncated hemoglobin / Truncated hemoglobin 1


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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.1370.21
2
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 1.8 M ammonium sulfate, 20% glycerol, 0.1 M glycine

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21102
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
SEALED TUBEOTHER21.5418
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELAug 15, 2014
AGILENT ATLAS CCD2CCDAug 15, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.54181
ReflectionResolution: 1.893→47.3 Å / Num. obs: 39522 / % possible obs: 99.86 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.0816 / Net I/σ(I): 13.81
Reflection shellResolution: 1.893→1.961 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 0.96 / % possible all: 98.97

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata scaling
SHELXphasing
SHELXDEphasing
CrysalisProdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.893→47.3 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 1993 5.05 %Random selection
Rwork0.1869 ---
obs0.1884 39472 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.893→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 86 209 2226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012075
X-RAY DIFFRACTIONf_angle_d1.1182825
X-RAY DIFFRACTIONf_dihedral_angle_d15.749741
X-RAY DIFFRACTIONf_chiral_restr0.046284
X-RAY DIFFRACTIONf_plane_restr0.005367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.893-1.94040.38571250.37822608X-RAY DIFFRACTION98
1.9404-1.99290.39371710.33572593X-RAY DIFFRACTION100
1.9929-2.05160.34091320.3172637X-RAY DIFFRACTION100
2.0516-2.11780.33191450.28032612X-RAY DIFFRACTION100
2.1178-2.19350.28881580.22132627X-RAY DIFFRACTION100
2.1935-2.28130.24361360.20322640X-RAY DIFFRACTION100
2.2813-2.38510.23151340.19112662X-RAY DIFFRACTION100
2.3851-2.51080.18051270.18662677X-RAY DIFFRACTION100
2.5108-2.66810.23151600.19872654X-RAY DIFFRACTION100
2.6681-2.87410.22731240.19242691X-RAY DIFFRACTION100
2.8741-3.16330.23961440.20532690X-RAY DIFFRACTION100
3.1633-3.62090.22151620.1842699X-RAY DIFFRACTION100
3.6209-4.56140.1871480.14812748X-RAY DIFFRACTION100
4.5614-47.31770.16441270.1622941X-RAY DIFFRACTION100
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)
17.86680.28761.05314.7519-1.41666.47970.05990.515-0.3483-0.52380.16790.76290.3463-0.1534-0.12740.3582-0.0085-0.05760.26060.11480.4901-34.66152.40216.8414
26.08430.34612.71315.3408-0.08661.37990.03680.4879-0.1337-0.50210.06920.30210.21960.3155-0.09140.3432-0.0191-0.01950.38470.0760.1921-22.032749.21197.9201
35.19052.64066.48767.59322.78788.05850.28780.2588-0.187-0.32460.01480.4230.62780.4659-0.44420.37260.00760.02820.30220.0220.2837-21.500840.109213.4006
44.8653-5.56215.93257.1704-6.2737.6663-0.3994-0.51450.08340.41520.42150.38-0.4086-0.1182-0.03450.3025-0.00470.0820.35910.06560.3674-29.286355.777817.9519
52.3436-2.05220.75117.75231.21760.9774-0.1956-0.3375-0.58810.47750.39020.94090.0216-0.1506-0.18250.3829-0.02120.13330.45340.23940.5015-32.605445.670620.4245
66.3915-5.39293.44318.0121-1.85195.4659-0.22290.51440.6493-1.02560.38930.245-0.6364-0.1313-0.09790.6286-0.1162-0.0110.57130.22540.5167-2.419862.84653.8578
77.06590.45021.22063.376-0.3122.9923-0.01641.03770.1451-0.79480.1652-0.38270.09310.4103-0.20120.4549-0.06440.12530.55630.02080.37444.726952.1511.6398
86.21230.62980.91876.70010.09913.1086-0.12140.5148-0.0103-0.40630.2069-0.20160.09440.1154-0.08660.2603-0.04760.05790.38860.03120.2072-0.336652.091110.9649
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 108 )
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 131 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 34 )
7X-RAY DIFFRACTION7chain 'B' and (resid 35 through 62 )
8X-RAY DIFFRACTION8chain 'B' and (resid 63 through 128 )

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