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- PDB-4rkm: Wolinella succinogenes octaheme sulfite reductase MccA, form I -

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Basic information

Entry
Database: PDB / ID: 4rkm
TitleWolinella succinogenes octaheme sulfite reductase MccA, form I
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
ACETATE ION / (R,R)-2,3-BUTANEDIOL / COPPER (I) ION / PROTOPORPHYRIN IX CONTAINING FE / SULFUR DIOXIDE / SULFUR OXIDE / Dissimilatory sulfite reductase MccA
Similarity search - Component
Biological speciesWolinella succinogenes DSM 1740 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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_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_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
E: MccA
F: MccA
H: MccA
I: MccA
J: MccA
K: MccA
L: MccA
G: MccA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,048,876173
Polymers985,05212
Non-polymers63,824161
Water52,8562934
1
A: MccA
B: MccA
C: MccA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,26644
Polymers246,2633
Non-polymers16,00341
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45050 Å2
ΔGint-597 kcal/mol
Surface area65750 Å2
MethodPISA
2
D: MccA
E: MccA
K: MccA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,12742
Polymers246,2633
Non-polymers15,86439
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44480 Å2
ΔGint-604 kcal/mol
Surface area65920 Å2
MethodPISA
3
F: MccA
I: MccA
J: MccA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,21843
Polymers246,2633
Non-polymers15,95440
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44600 Å2
ΔGint-599 kcal/mol
Surface area65540 Å2
MethodPISA
4
H: MccA
L: MccA
G: MccA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,26644
Polymers246,2633
Non-polymers16,00341
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44770 Å2
ΔGint-608 kcal/mol
Surface area65380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.121, 103.042, 233.070
Angle α, β, γ (deg.)90.00, 98.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 12 molecules ABCDEFHIJKLG

#1: Protein
MccA


Mass: 82087.703 Da / Num. of mol.: 12
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 , 7 types, 3095 molecules

#2: Chemical
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-SX / SULFUR OXIDE


Mass: 48.064 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: OS
#4: Chemical...
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical...
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 96 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#7: Chemical
ChemComp-SO2 / SULFUR DIOXIDE


Mass: 64.064 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2934 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.25
Details: 12% PEG 5000 MME, 0.1M HEPES/NaOH, 5% tacsimate pH 7.0, 4mM Zwittergent 3-12, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.381 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2014 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.381 Å / Relative weight: 1
ReflectionResolution: 2.2→49.37 Å / Num. obs: 500807 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.199 / Net I/σ(I): 9.2

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.37 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.059 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22011 24857 5 %RANDOM
Rwork0.18365 ---
all0.18546 500807 --
obs0.18546 475210 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å21.45 Å2
2---0.63 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms62698 0 4382 2934 70014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01969247
X-RAY DIFFRACTIONr_bond_other_d0.0020.0262613
X-RAY DIFFRACTIONr_angle_refined_deg1.3092.02794632
X-RAY DIFFRACTIONr_angle_other_deg0.7763144121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80957897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88224.2353060
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7521511343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.00515336
X-RAY DIFFRACTIONr_chiral_restr0.0920.29057
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0279291
X-RAY DIFFRACTIONr_gen_planes_other0.0050.0217173
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_it1.1813.89931636
X-RAY DIFFRACTIONr_mcbond_other1.1813.89931634
X-RAY DIFFRACTIONr_mcangle_it25.84339509
X-RAY DIFFRACTIONr_mcangle_other25.84339510
X-RAY DIFFRACTIONr_scbond_it1.2673.90737611
X-RAY DIFFRACTIONr_scbond_other1.2673.90637605
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.175.76355121
X-RAY DIFFRACTIONr_long_range_B_refined4.88335.954311957
X-RAY DIFFRACTIONr_long_range_B_other4.88335.954311958
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 1812 -
Rwork0.321 34964 -
obs--99.75 %

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