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- PDB-5h8v: Crystal structure of the complex between maize Sulfite Reductase ... -

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Basic information

Entry
Database: PDB / ID: 5h8v
TitleCrystal structure of the complex between maize Sulfite Reductase and ferredoxin in the form-1 crystal
ComponentsSulfite reductase [ferredoxin], chloroplastic
KeywordsOXIDOREDUCTASE / Ferredoxin / Sulfite reductase
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 cold ...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 cold / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / IRON/SULFUR CLUSTER / SIROHEME / Sulfite reductase [ferredoxin], chloroplastic
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsKurisu, G. / Nakayama, M. / Hase, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and Technology AgencyCREST Japan
Cabinet office of JapanGS016 Japan
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 24, 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_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_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 / _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 2.1Oct 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,98012
Polymers130,1562
Non-polymers2,82410
Water4,594255
1
A: Sulfite reductase [ferredoxin], chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4906
Polymers65,0781
Non-polymers1,4125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-50 kcal/mol
Surface area21920 Å2
MethodPISA
2
B: Sulfite reductase [ferredoxin], chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4906
Polymers65,0781
Non-polymers1,4125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-50 kcal/mol
Surface area21310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.346, 103.346, 255.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: _ / Auth seq-ID: 63 - 628 / Label seq-ID: 11 - 576

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#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)

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Non-polymers , 5 types, 265 molecules

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


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


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


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25.5 % PEG4000, 0.17M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2007
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 634871 / % possible obs: 99.4 % / Redundancy: 9 % / Net I/σ(I): 25.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→48.04 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / SU B: 9.553 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23857 2129 3 %RANDOM
Rwork0.19954 ---
obs0.20075 68424 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.636 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.2→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8877 0 156 255 9288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0199251
X-RAY DIFFRACTIONr_bond_other_d0.0050.028789
X-RAY DIFFRACTIONr_angle_refined_deg2.2281.99912662
X-RAY DIFFRACTIONr_angle_other_deg1.446320246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64651120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50224.279423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14151577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3481564
X-RAY DIFFRACTIONr_chiral_restr0.1160.21354
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02110464
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022084
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_it1.4191.7354492
X-RAY DIFFRACTIONr_mcbond_other1.4171.7354491
X-RAY DIFFRACTIONr_mcangle_it2.0762.5925608
X-RAY DIFFRACTIONr_mcangle_other2.0762.5925609
X-RAY DIFFRACTIONr_scbond_it2.0331.9474759
X-RAY DIFFRACTIONr_scbond_other2.0211.9474753
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1512.8276924
X-RAY DIFFRACTIONr_long_range_B_refined4.13914.01110516
X-RAY DIFFRACTIONr_long_range_B_other4.1413.9910460
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 35772 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 130 -
Rwork0.209 4759 -
obs--95.15 %
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)
10.3420.32220.08110.51410.01490.1855-0.0254-0.0277-0.0253-0.05630.0153-0.1048-0.0043-0.02680.01010.01340.00030.02520.0750.02570.068126.05963.83887.077
20.29420.0794-0.08370.19340.00950.1465-0.02230.0511-0.01030.01490.0040.0041-0.0309-0.04780.01830.01860.0108-0.00230.1465-0.00050.029683.58939.83787.527
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A63 - 703
2X-RAY DIFFRACTION2B63 - 703

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