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- PDB-7zs2: Diheme cytochrome c Kustd1711 from Kuenenia stuttgartiensis, M292... -

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Basic information

Entry
Database: PDB / ID: 7zs2
TitleDiheme cytochrome c Kustd1711 from Kuenenia stuttgartiensis, M292H mutant
ComponentsHypothetical (Diheme) protein
KeywordsELECTRON TRANSPORT / anaerobic ammonium oxidation
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding / membrane
Similarity search - Function
Haem-binding domain, putative / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / IMIDAZOLE / Hypothetical (Diheme) protein
Similarity search - Component
Biological speciesCandidatus Kuenenia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsAkram, M. / Barends, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Redox potential tuning by calcium ions in a novel c-type cytochrome from an anammox organism.
Authors: Akram, M. / Hauser, D. / Dietl, A. / Steigleder, M. / Ullmann, G.M. / Barends, T.R.M.
History
DepositionMay 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Sep 4, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _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_symmetry / _struct_mon_prot_cis.pdbx_omega_angle
Description: Atomic clashes / Details: Re-refined structure with better clashscore. / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.2Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.year
Revision 2.3Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical (Diheme) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7698
Polymers34,3021
Non-polymers1,4667
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-84 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.650, 92.710, 55.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Hypothetical (Diheme) protein / Putative (Diheme) protein


Mass: 34302.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Kuenenia (bacteria) / Gene: KsCSTR_07890, KSMBR1_1466, kustd1711 / Production host: Shewanella oneidensis MR-1 (bacteria) / References: UniProt: Q1PZE6
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M calcium acetate, 0.1 M imidazole/HCl pH 8.0 and 20% PEG 1K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99988 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 1.12→50 Å / Num. obs: 211675 / % possible obs: 88.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 14.58 Å2 / Rpim(I) all: 0.042 / Net I/σ(I): 15.4
Reflection shellResolution: 1.12→1.15 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4298 / Rpim(I) all: 0.892

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WT Structure

Resolution: 1.12→35.51 Å / SU ML: 0.0833 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 13.8013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1426 10582 5 %
Rwork0.1252 201002 -
obs0.1261 211584 88.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.21 Å2
Refinement stepCycle: LAST / Resolution: 1.12→35.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 95 485 2716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02072380
X-RAY DIFFRACTIONf_angle_d1.52313265
X-RAY DIFFRACTIONf_chiral_restr0.1223352
X-RAY DIFFRACTIONf_plane_restr0.0186419
X-RAY DIFFRACTIONf_dihedral_angle_d13.3905335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.12-1.130.34480.3523869X-RAY DIFFRACTION11.48
1.13-1.150.35171360.30922428X-RAY DIFFRACTION32.04
1.15-1.160.27822140.2654234X-RAY DIFFRACTION55.94
1.16-1.180.25482740.23024994X-RAY DIFFRACTION66.15
1.18-1.190.22262960.20865472X-RAY DIFFRACTION72.45
1.19-1.210.21263070.18995914X-RAY DIFFRACTION78.92
1.21-1.220.19233440.17546590X-RAY DIFFRACTION86.73
1.22-1.240.17833690.15896920X-RAY DIFFRACTION91.99
1.24-1.260.17173930.14147359X-RAY DIFFRACTION97.41
1.26-1.280.15983960.13587576X-RAY DIFFRACTION99.19
1.28-1.30.13873920.12687446X-RAY DIFFRACTION99.13
1.3-1.330.15253770.127480X-RAY DIFFRACTION98.93
1.33-1.350.14433940.11687488X-RAY DIFFRACTION98.76
1.35-1.380.12473830.11397443X-RAY DIFFRACTION98.64
1.38-1.410.14673920.11387439X-RAY DIFFRACTION98.45
1.41-1.440.15543880.10687441X-RAY DIFFRACTION98.32
1.44-1.480.13863880.09867405X-RAY DIFFRACTION98.35
1.48-1.520.11783940.09467515X-RAY DIFFRACTION98.64
1.52-1.570.11513950.09027518X-RAY DIFFRACTION99.79
1.57-1.620.12793910.09127522X-RAY DIFFRACTION99.63
1.62-1.670.12313990.09617580X-RAY DIFFRACTION99.63
1.67-1.740.12653930.09827507X-RAY DIFFRACTION99.05
1.74-1.820.12663950.10467377X-RAY DIFFRACTION98.35
1.82-1.920.13783920.117397X-RAY DIFFRACTION97.78
1.92-2.040.11883870.11397380X-RAY DIFFRACTION97.26
2.04-2.190.13393910.10957406X-RAY DIFFRACTION97.98
2.19-2.410.12483840.11447400X-RAY DIFFRACTION98.16
2.41-2.760.13963960.12987402X-RAY DIFFRACTION97.83
2.76-3.480.15613900.14027350X-RAY DIFFRACTION97.25
3.48-35.510.15223840.14547150X-RAY DIFFRACTION94.67

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