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- PDB-5h8y: Crystal structure of the complex between maize sulfite reductase ... -

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Basic information

Entry
Database: PDB / ID: 5h8y
TitleCrystal structure of the complex between maize sulfite reductase and ferredoxin in the form-2 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 activity / sulfite reductase (ferredoxin) activity / chloroplast nucleoid / stromule / sulfate assimilation / chloroplast stroma / response to light stimulus ...plastid chromosome packaging / assimilatory sulfite reductase (ferredoxin) / sulfide oxidation / sulfite reductase activity / sulfite reductase (ferredoxin) activity / chloroplast nucleoid / stromule / sulfate assimilation / chloroplast stroma / response to light stimulus / response to cold / 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 / 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: 2.2 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 2.0Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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 / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)287,01224
Polymers281,3486
Non-polymers5,66418
Water7,062392
1
A: Sulfite reductase [ferredoxin], chloroplastic
D: Sulfite reductase [ferredoxin], chloroplastic
E: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,50612
Polymers140,6743
Non-polymers2,8329
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sulfite reductase [ferredoxin], chloroplastic
C: Sulfite reductase [ferredoxin], chloroplastic
F: Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,50612
Polymers140,6743
Non-polymers2,8329
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.219, 176.219, 195.315
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSTRPTRPAA63 - 62811 - 576
21LYSLYSTRPTRPBB63 - 62811 - 576
12ARGARGTRPTRPAA64 - 62812 - 576
22ARGARGTRPTRPCC64 - 62812 - 576
13LYSLYSTRPTRPAA63 - 62811 - 576
23LYSLYSTRPTRPDD63 - 62811 - 576
14ARGARGTRPTRPBB64 - 62812 - 576
24ARGARGTRPTRPCC64 - 62812 - 576
15LYSLYSTRPTRPBB63 - 62811 - 576
25LYSLYSTRPTRPDD63 - 62811 - 576
16ARGARGTRPTRPCC64 - 62812 - 576
26ARGARGTRPTRPDD64 - 62812 - 576
17LEULEULEULEUEE25 - 9525 - 95
27LEULEULEULEUFF7 - 957 - 95

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

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Protein , 2 types, 6 molecules ABCDEF

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


Mass: 65077.895 Da / Num. of mol.: 4
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.: 2
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, 410 molecules

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


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


Mass: 916.661 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H44FeN4O16
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 22.5% PEG4000, 0.17 M 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: 2.2→50 Å / Num. obs: 1199152 / % possible obs: 100 % / Redundancy: 6.9 % / Net I/σ(I): 19.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30.07 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.894 / SU B: 10.766 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24682 8681 5 %RANDOM
Rwork0.21792 ---
obs0.21935 164856 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.586 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.02 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18928 0 300 392 19620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01919684
X-RAY DIFFRACTIONr_bond_other_d0.0080.0218588
X-RAY DIFFRACTIONr_angle_refined_deg2.2741.99626941
X-RAY DIFFRACTIONr_angle_other_deg1.729342827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.65852405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09924.408887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.052153303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.06315128
X-RAY DIFFRACTIONr_chiral_restr0.1330.22911
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02122308
X-RAY DIFFRACTIONr_gen_planes_other0.0090.024386
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_it1.5352.0349659
X-RAY DIFFRACTIONr_mcbond_other1.5342.0349658
X-RAY DIFFRACTIONr_mcangle_it2.293.04412051
X-RAY DIFFRACTIONr_mcangle_other2.293.04412052
X-RAY DIFFRACTIONr_scbond_it1.7922.15710025
X-RAY DIFFRACTIONr_scbond_other1.792.15710022
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7153.17814637
X-RAY DIFFRACTIONr_long_range_B_refined4.03616.322672
X-RAY DIFFRACTIONr_long_range_B_other4.02816.2722588
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A360000.1
12B360000.1
21A356190.11
22C356190.11
31A352450.1
32D352450.1
41B354510.11
42C354510.11
51B351390.11
52D351390.11
61C352840.1
62D352840.1
71E23890.24
72F23890.24
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 652 -
Rwork0.252 12102 -
obs--99.99 %
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)
10.613-0.09340.13490.5765-0.06970.7257-0.00950.009-0.0507-0.056-0.02020.1126-0.0759-0.12270.02970.06030.0474-0.04430.086-0.02560.0904-102.03470.9459.078
20.3767-0.04680.02240.4773-0.02020.6802-0.0553-0.0609-0.03460.01950.00040.07840.1322-0.02940.05480.10070.00910.04580.07980.01270.0853-76.63531.967-8.929
30.6715-0.10610.09821.1176-0.05130.99110.0671-0.02630.115-0.0676-0.0766-0.2597-0.16530.19280.00950.1076-0.0350.03960.0612-0.00230.0899-57.971-0.08924.609
41.3013-0.56860.10491.1792-0.35120.57590.01840.2150.2942-0.06-0.1359-0.4043-0.00730.18930.11750.0520.03610.02420.14310.07890.1572-119.282103.706-24.32
53.7368-1.67461.69844.311-0.71193.75890.7689-0.1759-0.2721-0.52820.17790.60770.3735-0.2894-0.94680.1817-0.0673-0.1020.14370.11250.3302-120.59659.378-16.638
68.81252.3585-5.86583.6166-3.850610.31510.0838-0.03240.1439-0.06590.60990.12750.3784-0.4937-0.69370.14790.00030.03840.27940.07810.133-98.33325.96816.518
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A62 - 628
2X-RAY DIFFRACTION1A701 - 703
3X-RAY DIFFRACTION2B63 - 628
4X-RAY DIFFRACTION2B701 - 703
5X-RAY DIFFRACTION3C64 - 628
6X-RAY DIFFRACTION3C701 - 703
7X-RAY DIFFRACTION4D63 - 628
8X-RAY DIFFRACTION4D701 - 703
9X-RAY DIFFRACTION5E1 - 96
10X-RAY DIFFRACTION5E101
11X-RAY DIFFRACTION6F7 - 96
12X-RAY DIFFRACTION6F101

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