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- PDB-6nx0: Crystal structure of the diheme peroxidase BthA from Burkholderia... -

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Basic information

Entry
Database: PDB / ID: 6nx0
TitleCrystal structure of the diheme peroxidase BthA from Burkholderia thailandensis E264
ComponentsDi-haem cytochrome c peroxidase family protein
KeywordsOXIDOREDUCTASE / heme / peroxidase / diheme
Function / homology
Function and homology information


peroxidase activity / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Di-haem cytochrome c peroxidase / Di-haem cytochrome c peroxidase / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
HEME C / NITRATE ION / Di-haem cytochrome c peroxidase family protein
Similarity search - Component
Biological speciesBurkholderia thailandensis E264 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsCohen, S.E. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)126982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)008334 United States
CitationJournal: Nat Commun / Year: 2019
Title: A widely distributed diheme enzyme from Burkholderia that displays an atypically stable bis-Fe(IV) state.
Authors: Rizzolo, K. / Cohen, S.E. / Weitz, A.C. / Lopez Munoz, M.M. / Hendrich, M.P. / Drennan, C.L. / Elliott, S.J.
History
DepositionFeb 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Di-haem cytochrome c peroxidase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,04611
Polymers51,3361
Non-polymers1,71010
Water9,800544
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.210, 84.776, 95.831
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 Di-haem cytochrome c peroxidase family protein


Mass: 51335.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis E264 (bacteria)
Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264 / Gene: BTH_II1092 / Plasmid: pETSN / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2T6B0

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Non-polymers , 5 types, 554 molecules

#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.03 Å3/Da / Density % sol: 39.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 300 mM ammonium nitrate, 22% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 62412 / % possible obs: 99.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.038 / Rrim(I) all: 0.106 / Χ2: 0.961 / Net I/σ(I): 5.8 / Num. measured all: 468091
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.54-1.65.30.74561200.7050.3440.8240.93799
1.6-1.667.20.6261770.8530.2450.6680.94799.9
1.66-1.737.80.49361470.9050.1870.5280.96199.8
1.73-1.837.70.35961910.9460.1380.3850.96299.8
1.83-1.947.40.24461970.970.0950.2630.99899.8
1.94-2.098.20.17462130.9860.0650.1861.02100
2.09-2.37.90.12362370.9910.0460.1321.01199.6
2.3-2.637.80.08762540.9950.0330.0931.01499.8
2.63-3.3280.06563100.9980.0240.0690.94299.4
3.32-507.70.04765660.9980.0180.050.80799.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3l4m

3l4m


Resolution: 1.54→47.916 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.77
RfactorNum. reflection% reflection
Rfree0.1796 3118 5 %
Rwork0.1503 --
obs0.1518 62344 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66 Å2 / Biso mean: 19.569 Å2 / Biso min: 7.01 Å2
Refinement stepCycle: final / Resolution: 1.54→47.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 186 544 3879
Biso mean--15.48 28.55 -
Num. residues----413
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5389-1.5630.26591370.24112593273097
1.563-1.58860.26041370.2272618275599
1.5886-1.6160.22951400.205626652805100
1.616-1.64540.25081420.195726732815100
1.6454-1.6770.25271400.188626772817100
1.677-1.71120.23671410.18226642805100
1.7112-1.74850.22941380.17992646278499
1.7485-1.78910.18611420.167626942836100
1.7891-1.83390.18511410.160626752816100
1.8339-1.88350.19121410.154526792820100
1.8835-1.93890.17541400.151426662806100
1.9389-2.00150.18951410.154126832824100
2.0015-2.0730.16181420.144326862828100
2.073-2.1560.15631430.140727122855100
2.156-2.25410.16361410.13872671281299
2.2541-2.3730.171410.135226982839100
2.373-2.52160.16311420.131626982840100
2.5216-2.71630.15351440.13727232867100
2.7163-2.98960.16161440.140327322876100
2.9896-3.42210.19171430.13722723286699
3.4221-4.31110.15721460.126827812927100
4.3111-47.93870.17821520.16292869302199

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