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- PDB-4rkn: Wolinella succinogenes octaheme sulfite reductase MccA, form II -

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Basic information

Entry
Database: PDB / ID: 4rkn
TitleWolinella succinogenes octaheme sulfite reductase MccA, form II
ComponentsMccA
KeywordsUNKNOWN FUNCTION / multiheme cytochrome c / sulfite reductase / periplasmic
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors; With unknown physiological acceptors / oxidoreductase activity, acting on a sulfur group of donors / sulfite reductase activity / hydrogen sulfide biosynthetic process / anaerobic respiration / protein homotrimerization / cuprous ion binding / periplasmic space / heme binding / identical protein binding
Similarity search - Function
Dissimilatory sulfite reductase / : / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily
Similarity search - Domain/homology
COPPER (II) ION / DITHIONITE / PROTOPORPHYRIN IX CONTAINING FE / SULFITE ION / Dissimilatory sulfite reductase MccA
Similarity search - Component
Biological speciesWolinella succinogenes DSM 1740 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsHermann, B. / Kern, M. / La Pietra, L. / Simon, J. / Einsle, O.
CitationJournal: Nature / Year: 2015
Title: The octahaem MccA is a haem c-copper sulfite reductase.
Authors: Hermann, B. / Kern, M. / La Pietra, L. / Simon, J. / Einsle, O.
History
DepositionOct 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Jun 24, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _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: MccA
B: MccA
C: MccA
D: MccA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)349,37450
Polymers328,3514
Non-polymers21,02346
Water25,5631419
1
A: MccA
B: MccA
C: MccA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,00237
Polymers246,2633
Non-polymers15,73934
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11910 Å2
ΔGint-14 kcal/mol
Surface area75990 Å2
MethodPISA
2
D: MccA
hetero molecules

D: MccA
hetero molecules

D: MccA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,11439
Polymers246,2633
Non-polymers15,85136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area12080 Å2
ΔGint-13 kcal/mol
Surface area75710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.472, 186.472, 232.836
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11D-1402-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
MccA


Mass: 82087.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: C-terminal double-StrepTag(II)
Source: (gene. exp.) Wolinella succinogenes DSM 1740 (bacteria)
Strain: ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W
Gene: mcca, WS0379 / Production host: Wolinella succinogenes (bacteria) / References: UniProt: Q7MSJ8

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Non-polymers , 5 types, 1465 molecules

#2: Chemical
ChemComp-DTN / DITHIONITE


Mass: 128.128 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: O4S2
#3: Chemical...
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#5: Chemical
ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1419 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 15% PEG 3350, 0.1 M CHES/NaOH, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.7389 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7389 Å / Relative weight: 1
ReflectionResolution: 2.1→47.26 Å / Num. all: 176117 / Num. obs: 175765 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 17.3

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→47.26 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.372 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17517 8789 5 %RANDOM
Rwork0.13465 ---
all0.1366 176117 --
obs0.13666 166976 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.761 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20910 0 1430 1419 23759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01923351
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220969
X-RAY DIFFRACTIONr_angle_refined_deg1.9212.03631992
X-RAY DIFFRACTIONr_angle_other_deg0.958348263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55652657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44924.2521023
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.599153795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.12915112
X-RAY DIFFRACTIONr_chiral_restr0.1480.23035
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0226904
X-RAY DIFFRACTIONr_gen_planes_other0.0110.025832
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_it2.0722.48410598
X-RAY DIFFRACTIONr_mcbond_other2.0712.48310597
X-RAY DIFFRACTIONr_mcangle_it2.8253.71113256
X-RAY DIFFRACTIONr_mcangle_other2.8253.71113257
X-RAY DIFFRACTIONr_scbond_it3.0222.6712753
X-RAY DIFFRACTIONr_scbond_other32.66912731
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5143.84618712
X-RAY DIFFRACTIONr_long_range_B_refined5.93523.39106183
X-RAY DIFFRACTIONr_long_range_B_other5.87223.327105124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 679 -
Rwork0.184 11991 -
obs--97.37 %

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