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- PDB-6i5b: Crystal Structure of Outer Cell Wall Cytochrome OcwA -

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Basic information

Entry
Database: PDB / ID: 6i5b
TitleCrystal Structure of Outer Cell Wall Cytochrome OcwA
ComponentsUncharacterized protein
KeywordsOXIDOREDUCTASE / multiheme c-type cytochromes / surface exposed proteins / Gram-positive bacteria / Thermincola potens JR / extracellular electron transfer
Function / homology
Function and homology information


nitrite reductase (cytochrome, ammonia-forming) activity / periplasmic space / metal ion binding
Similarity search - Function
Cytochrome c-552/4 / Cytochrome c554 and c-prime / Cytochrome c552 / Cytochrome c552 / Multiheme cytochrome superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / HEME C / Cytochrome c-552/4 domain-containing protein
Similarity search - Component
Biological speciesThermincola potens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsHermann, B. / Einsle, O.
CitationJournal: Mbio / Year: 2019
Title: How Thermophilic Gram-Positive Organisms Perform Extracellular Electron Transfer: Characterization of the Cell Surface Terminal Reductase OcwA.
Authors: Costa, N.L. / Hermann, B. / Fourmond, V. / Faustino, M.M. / Teixeira, M. / Einsle, O. / Paquete, C.M. / Louro, R.O.
History
DepositionNov 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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_ncs_dom_lim
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,05523
Polymers113,7722
Non-polymers11,28321
Water3,063170
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23180 Å2
ΔGint-408 kcal/mol
Surface area42610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.855, 62.969, 84.210
Angle α, β, γ (deg.)101.54, 99.13, 98.41
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 43 - 524 / Label seq-ID: 14 - 495

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized protein


Mass: 56886.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 9 heme c groups, one Mg and one Cl
Source: (gene. exp.) Thermincola potens (strain JR) (bacteria)
Strain: JR / Gene: TherJR_2595 / Production host: Escherichia coli (E. coli) / References: UniProt: D5XBK3

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Non-polymers , 5 types, 191 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 100 mM magnesium chloride, 100 mM HEPES/ NaOH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→80.94 Å / Num. obs: 53356 / % possible obs: 98.1 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.047 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.29 / Num. unique obs: 4603 / CC1/2: 0.4 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→80.94 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 9.928 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23337 2643 5 %RANDOM
Rwork0.20269 ---
obs0.20428 50713 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.672 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å21.82 Å20.2 Å2
2---0.67 Å2-1.93 Å2
3----1.8 Å2
Refinement stepCycle: 1 / Resolution: 2.2→80.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7326 0 782 170 8278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.028455
X-RAY DIFFRACTIONr_bond_other_d0.0020.027329
X-RAY DIFFRACTIONr_angle_refined_deg1.4162.07911659
X-RAY DIFFRACTIONr_angle_other_deg0.9993.00417001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.115965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.65325.691311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.354151251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1158
X-RAY DIFFRACTIONr_chiral_restr0.120.21115
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219613
X-RAY DIFFRACTIONr_gen_planes_other0.010.021735
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_it2.7425.9343866
X-RAY DIFFRACTIONr_mcbond_other2.7425.9323865
X-RAY DIFFRACTIONr_mcangle_it4.4948.8964829
X-RAY DIFFRACTIONr_mcangle_other4.4948.8974830
X-RAY DIFFRACTIONr_scbond_it2.5435.8954589
X-RAY DIFFRACTIONr_scbond_other2.5435.8954587
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1658.7066830
X-RAY DIFFRACTIONr_long_range_B_refined6.45665.1919949
X-RAY DIFFRACTIONr_long_range_B_other6.44365.199932
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 29132 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 180 -
Rwork0.367 3712 -
obs--97.23 %

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