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- PDB-5e37: Redox protein from Chlamydomonas reinhardtii -

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Basic information

Entry
Database: PDB / ID: 5.0E+37
TitleRedox protein from Chlamydomonas reinhardtii
ComponentsEF-Hand domain-containing thioredoxin
KeywordsOXIDOREDUCTASE / Calredoxin / calcium- / redox- / Chlamydomonas reinhardtii
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
Thioredoxin / EF-hand / Thioredoxin domain profile. / Recoverin; domain 1 / Thioredoxin domain / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...Thioredoxin / EF-hand / Thioredoxin domain profile. / Recoverin; domain 1 / Thioredoxin domain / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Thioredoxin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
EF-Hand domain-containing thioredoxin
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCharoenwattansatien, R. / Hochmal, A.K. / Zinzius, K. / Muto, R. / Tanaka, H. / Hippler, M. / Kurisu, G.
Funding support Japan, 2items
OrganizationGrant numberCountry
Funding Program for Next Generation World-Leading Researchers from the Cabinet Office of JapanGS016 Japan
International Joint Research Promotion Program and International Collaborative Research Program, Osaka University Japan
CitationJournal: Nat Commun / Year: 2016
Title: Calredoxin represents a novel type of calcium-dependent sensor-responder connected to redox regulation in the chloroplast
Authors: Hochmal, A.K. / Zinzius, K. / Charoenwattanasatien, R. / Gabelein, P. / Mutoh, R. / Tanaka, H. / Schulze, S. / Liu, G. / Scholz, M. / Nordhues, A. / Offenborn, J.N. / Petroutsos, D. / ...Authors: Hochmal, A.K. / Zinzius, K. / Charoenwattanasatien, R. / Gabelein, P. / Mutoh, R. / Tanaka, H. / Schulze, S. / Liu, G. / Scholz, M. / Nordhues, A. / Offenborn, J.N. / Petroutsos, D. / Finazzi, G. / Fufezan, C. / Huang, K. / Kurisu, G. / Hippler, M.
History
DepositionOct 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EF-Hand domain-containing thioredoxin
C: EF-Hand domain-containing thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,22110
Polymers79,9012
Non-polymers3218
Water15,295849
1
A: EF-Hand domain-containing thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1115
Polymers39,9501
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: EF-Hand domain-containing thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1115
Polymers39,9501
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.960, 55.190, 89.580
Angle α, β, γ (deg.)90.00, 101.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EF-Hand domain-containing thioredoxin


Mass: 39950.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLREDRAFT_205510 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: A8IXH4*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 849 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. THE SEQUENCE IS FROM PHYTOZOME DATABASE, CRE03.G202950.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1.5 M LiSO4 in 0.1 M MES-NaOH buffer pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 108097 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 35.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.558 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.794 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23251 5367 4.9 %RANDOM
Rwork0.19879 ---
obs0.20046 103272 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.518 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4853 0 8 849 5710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0194947
X-RAY DIFFRACTIONr_bond_other_d0.0020.024694
X-RAY DIFFRACTIONr_angle_refined_deg2.2261.9796660
X-RAY DIFFRACTIONr_angle_other_deg1.126310846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93825.2225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62115910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7921524
X-RAY DIFFRACTIONr_chiral_restr0.1370.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025575
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021061
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_it2.6252.2822493
X-RAY DIFFRACTIONr_mcbond_other2.6222.2812492
X-RAY DIFFRACTIONr_mcangle_it3.6673.4153111
X-RAY DIFFRACTIONr_mcangle_other3.6673.4163112
X-RAY DIFFRACTIONr_scbond_it3.7832.6062454
X-RAY DIFFRACTIONr_scbond_other3.7822.6072455
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6073.7643550
X-RAY DIFFRACTIONr_long_range_B_refined7.26822.80922581
X-RAY DIFFRACTIONr_long_range_B_other7.04622.24121531
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 394 -
Rwork0.258 7606 -
obs--99.84 %

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