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- PDB-5h92: Crystal structure of the complex between maize Sulfite Reductase ... -

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Basic information

Entry
Database: PDB / ID: 5h92
TitleCrystal structure of the complex between maize Sulfite Reductase and ferredoxin in the form-3 crystal
Components
  • Ferredoxin-1, chloroplastic
  • Sulfite reductase [ferredoxin], chloroplastic
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / Ferredoxin / Sulfite reductase / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Function / homology
Function and homology information


plastid chromosome packaging / assimilatory sulfite reductase (ferredoxin) / sulfide oxidation / sulfite reductase (ferredoxin) activity / chloroplast nucleoid / sulfate assimilation / chloroplast stroma / response to light stimulus / chloroplast / electron transport chain ...plastid chromosome packaging / assimilatory sulfite reductase (ferredoxin) / sulfide oxidation / sulfite reductase (ferredoxin) activity / chloroplast nucleoid / sulfate assimilation / chloroplast stroma / response to light stimulus / chloroplast / electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / electron transfer activity / negative regulation of DNA-templated transcription / heme binding / DNA binding / metal ion binding
Similarity search - Function
Sulphite reductase, ferredoxin dependent / Nitrite and sulphite reductase 4Fe-4S domain containing protein / Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily / Nitrite and sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like half domain / Sulfite Reductase Hemoprotein; domain 1 ...Sulphite reductase, ferredoxin dependent / Nitrite and sulphite reductase 4Fe-4S domain containing protein / Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site / Nitrite and sulfite reductases iron-sulfur/siroheme-binding site. / Nitrite/Sulfite reductase ferredoxin-like domain / Nitrite/sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like domain superfamily / Nitrite and sulphite reductase 4Fe-4S domain / Nitrite/Sulfite reductase ferredoxin-like half domain / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / PHOSPHATE ION / IRON/SULFUR CLUSTER / SIROHEME / Sulfite reductase [ferredoxin], chloroplastic / Ferredoxin-1, chloroplastic
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsKurisu, G. / Nakayama, M. / Hase, T.
CitationJournal: J.Biochem. / Year: 2016
Title: Structural and mutational studies of an electron transfer complex of maize sulfite reductase and ferredoxin.
Authors: Kim, J.Y. / Nakayama, M. / Toyota, H. / Kurisu, G. / Hase, T.
History
DepositionDec 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 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 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id
Revision 2.0Dec 27, 2023Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfite reductase [ferredoxin], chloroplastic
B: Sulfite reductase [ferredoxin], chloroplastic
C: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,62512
Polymers140,6743
Non-polymers2,9519
Water6,864381
1
A: Sulfite reductase [ferredoxin], chloroplastic
C: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1607
Polymers75,5962
Non-polymers1,5635
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sulfite reductase [ferredoxin], chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4655
Polymers65,0781
Non-polymers1,3884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.414, 103.406, 122.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein Sulfite reductase [ferredoxin], chloroplastic / ZmSiR


Mass: 65077.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: SIR / Production host: Escherichia coli (E. coli)
References: UniProt: O23813, assimilatory sulfite reductase (ferredoxin)
#2: Protein Ferredoxin-1, chloroplastic / Ferredoxin I / Fd I


Mass: 10518.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: FDX1, pFD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P27787

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Non-polymers , 6 types, 390 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-SRM / SIROHEME


Mass: 916.661 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H44FeN4O16
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 28% PEG4000, 0.05M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 20, 2007
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 579880 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 34.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H8V

5h8v


Resolution: 2.08→43.27 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.06 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23189 3972 5 %RANDOM
Rwork0.17949 ---
obs0.18212 75136 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.295 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.12 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.08→43.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9618 0 158 381 10157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229999
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.98813616
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4151232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85924.509448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.462151654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.191562
X-RAY DIFFRACTIONr_chiral_restr0.1290.21486
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027650
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.24830
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.26899
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2574
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1370.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0741.56316
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61129916
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.81334237
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9474.53670
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.081→2.135 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 271 -
Rwork0.188 5374 -
obs--97.73 %
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)
10.4767-0.0985-0.05530.62860.12280.48440.0113-0.01920.04940.0254-0.0160.0537-0.0444-0.00870.00470.02820.0061-0.0099-0.21750.0031-0.232413.536.20222.574
21.2482-0.35840.27450.9784-0.17760.58450.0471-0.0274-0.2657-0.08710.02150.13210.02680.0282-0.0687-0.06940.0128-0.0217-0.2557-0.0084-0.132538.351-39.47321.653
31.3992.16713.116712.5348-1.521411.3364-0.00020.3875-0.07120.6686-0.2349-0.16630.12830.58580.23520.442-0.0233-0.0330.3983-0.00730.410124.69834.7416.723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A63 - 628
2X-RAY DIFFRACTION1A701 - 704
3X-RAY DIFFRACTION2B63 - 628
4X-RAY DIFFRACTION2B701 - 704
5X-RAY DIFFRACTION3C1 - 91
6X-RAY DIFFRACTION3C101

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