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- PDB-1aop: SULFITE REDUCTASE STRUCTURE AT 1.6 ANGSTROM RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1aop
TitleSULFITE REDUCTASE STRUCTURE AT 1.6 ANGSTROM RESOLUTION
ComponentsSULFITE REDUCTASE HEMOPROTEIN
KeywordsOXIDOREDUCTASE / SIROHEME / [4FE-4S] / SNIRR / SIX-ELECTRON REDUCTION / PHOSPHATE COMPLEX
Function / homology
Function and homology information


assimilatory sulfite reductase (NADPH) / sulfite reductase (NADPH) activity / sulfite reductase complex (NADPH) / 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
Sulfite Reductase Hemoprotein;Domain 2 / Sulphite reductase (NADPH) hemoprotein, beta subunit / 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 ...Sulfite Reductase Hemoprotein;Domain 2 / Sulphite reductase (NADPH) hemoprotein, beta subunit / 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 / Sulfite Reductase Hemoprotein; domain 1 / Sulfite Reductase Hemoprotein, domain 1 / Nitrite and sulphite reductase 4Fe-4S domain-like superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / IRON/SULFUR CLUSTER / SIROHEME / Sulfite reductase [NADPH] hemoprotein beta-component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD/MIR / Resolution: 1.6 Å
AuthorsCrane, B.R. / Getzoff, E.D.
Citation
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.
#1: Journal: Biochemistry / Year: 1997
Title: Structures of the Siroheme-and Fe4S4-Containing Active Center of Sulfite Reductase in Different States of Oxidation: Heme Activation Via Reduction-Gated Exogenous Ligand Exchange
Authors: Crane, B.R. / Siegel, L.M. / Getzoff, E.D.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Multiwavelength Anomalous Diffraction of Sulfite Reductase Hemoprotein: Making the Most of MAD Data
Authors: Crane, B.R. / Bellamy, H. / Getzoff, E.D.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Determining Phases and Anomalous-Scattering Models from the Multiwavelength Anomalous Diffraction of Native Protein Metal Clusters. Improved MAD Phase Error Estimates and Anomalous-Scatterer Positions
Authors: Crane, B.R. / Getzoff, E.D.
#4: Journal: J.Biol.Chem. / Year: 1989
Title: Characterization of the Cysjih Regions of Salmonella Typhimurium and Escherichia Coli B. DNA Sequences of Cysi and Cysh and a Model for the Siroheme-Fe4S4 Active Center of Sulfite Reductase ...Title: Characterization of the Cysjih Regions of Salmonella Typhimurium and Escherichia Coli B. DNA Sequences of Cysi and Cysh and a Model for the Siroheme-Fe4S4 Active Center of Sulfite Reductase Hemoprotein Based on Amino Acid Homology with Spinach Nitrite Reductase
Authors: Ostrowski, J. / Wu, J.Y. / Rueger, D.C. / Miller, B.E. / Siegel, L.M. / Kredich, N.M.
#5: Journal: J.Biol.Chem. / Year: 1986
Title: The Heme and Fe4S4 Cluster in the Crystallographic Structure of Escherichia Coli Sulfite Reductase
Authors: Mcree, D.E. / Richardson, D.C. / Richardson, J.S. / Siegel, L.M.
History
DepositionJul 8, 1997Processing site: BNL
SupersessionDec 24, 1997ID: 1GEO
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Refinement description
Category: pdbx_database_status / software ...pdbx_database_status / software / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site / _software.name
Revision 2.0Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer 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_site
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SULFITE REDUCTASE HEMOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1505
Polymers55,7481
Non-polymers1,4024
Water8,755486
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
Details: OXIDIZED, SIROHEME FE(III), [4FE-4S], +2 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B
Description: PBR322 DERIVATIVE CONTAINING ESCHERICHIA COLI CYSIJ AND S. TYPHIMURIUM CYSG UNDER CONTROL OF CYSJIH PROMOTER EXPRESSED IN A S. TYPHIMURIUM CYSI AUXOTROPH
Gene: CYSIJ / Plasmid: PJYW613 / Production host: Escherichia coli (E. coli)
References: UniProt: P17846, assimilatory sulfite reductase (NADPH)

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Non-polymers , 5 types, 490 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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


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


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


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsOXIDIZED, SIROHEME FE(III), [4FE-4S], +2.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.7 / Details: pH 7.7
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
265 mMpotassium phosphate1reservoir
30.1 MEDTA1reservoir
415 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 11, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 61005 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.099 / Net I/σ(I): 28.7
Reflection shellResolution: 1.6→1.76 Å / Mean I/σ(I) obs: 7.5 / Rsym value: 0.278 / % possible all: 93.5
Reflection
*PLUS
Rmerge(I) obs: 0.099
Reflection shell
*PLUS
% possible obs: 93.5 % / Rmerge(I) obs: 0.278

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MAD/MIR / Resolution: 1.6→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.218 --
Rwork0.182 --
obs0.182 61005 96.6 %
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20 Å2
2--3.18 Å20 Å2
3----1.69 Å2
Refine analyzeLuzzati sigma a obs: 0.14 Å
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3590 0 77 486 4153
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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: 1.6→1.76 Å
RfactorNum. reflection% reflection
Rwork0.278 7058 -
obs--93.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X_PO4_2.SRMTOPH19_SO3.FS4
X-RAY DIFFRACTION2PARHCSDX_SO3.PROTOPHCSDX_SO3.PRO
X-RAY DIFFRACTION3PARAM19X_SO3_2.SRMTOPH19_PO4.FS4
X-RAY DIFFRACTION4PARHCSDX_2_PO4.PRTOPH19_PO4.SR
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.278

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