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- PDB-8gep: SULFITE REDUCTASE HEMOPROTEIN NITRATE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 8gep
TitleSULFITE REDUCTASE HEMOPROTEIN NITRATE COMPLEX
ComponentsSULFITE REDUCTASE HEMOPROTEIN
KeywordsOXIDOREDUCTASE / SIROHEME FEIII OR FEII / [4FE-4S] +2 / NITRATE COMPLEX / INHIBITOR
Function / homology
Function and homology information


assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfite reductase (ferredoxin) activity / sulfite reductase complex (NADPH) / sulfite reductase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / NADP binding / 4 iron, 4 sulfur cluster binding ...assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfite reductase (ferredoxin) activity / sulfite reductase complex (NADPH) / sulfite reductase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / NADP binding / 4 iron, 4 sulfur cluster binding / heme binding / metal ion binding
Similarity search - Function
Sulphite reductase (NADPH) hemoprotein, beta subunit / Sulfite Reductase Hemoprotein;Domain 2 / Nitrite and sulphite reductase 4Fe-4S domain containing protein / Sulfite Reductase Hemoprotein; domain 2 / 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 ...Sulphite reductase (NADPH) hemoprotein, beta subunit / Sulfite Reductase Hemoprotein;Domain 2 / Nitrite and sulphite reductase 4Fe-4S domain containing protein / Sulfite Reductase Hemoprotein; domain 2 / 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 / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NITRATE ION / IRON/SULFUR CLUSTER / SIROHEME / Sulfite reductase [NADPH] hemoprotein beta-component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCrane, B.R. / Getzoff, E.D.
Citation
Journal: Biochemistry / Year: 1997
Title: Probing the catalytic mechanism of sulfite reductase by X-ray crystallography: structures of the Escherichia coli hemoprotein in complex with substrates, inhibitors, intermediates, and products.
Authors: Crane, B.R. / Siegel, L.M. / Getzoff, E.D.
#1: Journal: Science / Year: 1995
Title: Sulfite Reductase Structure at 1.6 A: Evolution and Catalysis for Reduction of Inorganic Anions
Authors: Crane, B.R. / Siegel, L.M. / Getzoff, E.D.
History
DepositionJul 11, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SULFITE REDUCTASE HEMOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1175
Polymers55,7481
Non-polymers1,3694
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.800, 77.400, 87.800
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 , 1 types, 1 molecules A

#1: Protein SULFITE REDUCTASE HEMOPROTEIN / SIRHP


Mass: 55747.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B
Description: PBR322 DERIVATIVE CONTAINING ESCHERICHIA COLI CYSIJ AND S. TYPHIMURIUM CYSG UNDER CONTROL OF THE CYSJIH PROMOTOR EXPRESSED IN A S. TYPHIMURIUM CYSI AUXOTROPH
Gene: CYSIJ / Plasmid: PJYW613 / Gene (production host): CYSIJ / Production host: Salmonella typhimurium (bacteria) / Strain (production host): CYSI68
References: UniProt: P17846, assimilatory sulfite reductase (NADPH)

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Non-polymers , 5 types, 339 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-SRM / SIROHEME / Siroheme


Mass: 916.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H44FeN4O16
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 40 % / Description: CRYSTALS ARE ISOMORPHOUS WITH THOSE FOR 1AOP
Crystal growpH: 7.7
Details: pH 7.7 OXIDIZED CRYSTALS WERE TREATED WITH HYDROXYLAMINE TO FORM THE NITRATE COMPLEX. SIROHEME HAS EITHER FEIII OR FEII AND [4FE-4S] CLUSTER IS +2. THE NITRATE BINDS IN THE ACTIVE SITE BUT ...Details: pH 7.7 OXIDIZED CRYSTALS WERE TREATED WITH HYDROXYLAMINE TO FORM THE NITRATE COMPLEX. SIROHEME HAS EITHER FEIII OR FEII AND [4FE-4S] CLUSTER IS +2. THE NITRATE BINDS IN THE ACTIVE SITE BUT DOES NOT COORDINATE THE SIROHEME IRON. THIS IS NAMED HP-NO3 IN THE PRIMARY REFERENCE.
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
265 mMpotassium phosphate1reservoir
30.1 MEDTA1reservoir
415 %PEGMW80001reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 19, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 22966 / % possible obs: 92.8 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 16.3 Å2 / Rsym value: 0.077 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.4 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.338 / % possible all: 83.5
Reflection
*PLUS
Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 83.5 % / Rmerge(I) obs: 0.338

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MARXDSdata reduction
MARSCALEdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AOP

1aop


Resolution: 2.2→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.189 --
obs0.189 22130 90.5 %
Displacement parametersBiso mean: 12.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2--0.79 Å20 Å2
3---0.5 Å2
Refine analyzeLuzzati d res low obs: 4 Å / Luzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3590 0 76 335 4001
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å
RfactorNum. reflection% reflection
Rwork0.239 2377 -
obs--79.7 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.239

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