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- PDB-5nku: Joint neutron/X-ray structure of dimeric chlorite dismutase from ... -

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Basic information

Entry
Database: PDB / ID: 5nku
TitleJoint neutron/X-ray structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425
ComponentsChlorite Dismutase
KeywordsOXIDOREDUCTASE / chlorite dismutase / cyanobacteria / heme / ferredoxin-like fold
Function / homology
Function and homology information


oxidoreductase activity / heme binding / metal ion binding
Similarity search - Function
Alpha-Beta Plaits - #3420 / Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / HYDROXIDE ION / Chlorite dismutase
Similarity search - Component
Biological speciesCyanothece sp.
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPuehringer, D. / Schaffner, I. / Mlynek, G. / Obinger, C. / Djinovic-Carugo, K.
CitationJournal: ACS Catal / Year: 2017
Title: Molecular Mechanism of Enzymatic Chlorite Detoxification: Insights from Structural and Kinetic Studies.
Authors: Schaffner, I. / Mlynek, G. / Flego, N. / Puhringer, D. / Libiseller-Egger, J. / Coates, L. / Hofbauer, S. / Bellei, M. / Furtmuller, P.G. / Battistuzzi, G. / Smulevich, G. / Djinovic-Carugo, K. / Obinger, C.
History
DepositionApr 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 2.0Nov 14, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site_gen.label_asym_id
Revision 2.1May 1, 2024Group: 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 / reflns_shell / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chlorite Dismutase
B: Chlorite Dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0568
Polymers43,6622
Non-polymers1,3956
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-72 kcal/mol
Surface area16070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.427, 53.015, 55.337
Angle α, β, γ (deg.)107.30, 98.54, 109.86
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Chlorite Dismutase /


Mass: 21830.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanothece sp. (strain PCC 7425 / ATCC 29141) (bacteria)
Strain: PCC 7425 / ATCC 29141 / Gene: Cyan7425_1434 / Plasmid: pEt-52b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: B8HNS6

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Non-polymers , 5 types, 116 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.52 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 6.5
Details: 0.15 M MgSO4, 0.1 M MES pH 6.5, 30% PEG 3350 grown in capillary counter-diffusion set up and buffer exchanged for 0.15 M MgSO4, 0.1 M Tris HCl pH 9.0, 30% PEG 3350, all dissolved in D2O.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
NUCLEAR REACTORORNL Spallation Neutron Source MANDI12.00 - 4.00
ROTATING ANODERIGAKU MICROMAX-007 HF21.54
Detector
TypeIDDetectorDate
ORNL ANGER CAMERA1CCDNov 30, 2015
RIGAKU RAXIS IV++2IMAGE PLATENov 30, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
121
241
31.541
Reflection

Biso Wilson estimate: 25.74 Å2 / Entry-ID: 5NKU / Diffraction-ID: 1 / Redundancy: 2.6 %

Resolution (Å)Num. obs% possible obs (%)Net I/σ(I)
2-19.4892798880.65.6
2.35-17.2231429266.77.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2689: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
Mantiddata processing
Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 3QPI

3qpi

/ Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)SU MLCross valid methodσ(F)Phase error
2-19.489X-RAY DIFFRACTION0.18590.14040.14251307279834.6780.650.2FREE R-VALUE1.9720.33
2.35-17.223NEUTRON DIFFRACTION0.25330.23940.24662142924.6366.890.4131.18
Refinement stepCycle: LAST / Resolution: 2→19.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2947 0 95 110 3152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0177017
X-RAY DIFFRACTIONf_angle_d1.6312348
X-RAY DIFFRACTIONf_dihedral_angle_d15.9872580
X-RAY DIFFRACTIONf_chiral_restr0.09432
X-RAY DIFFRACTIONf_plane_restr0.0081311
NEUTRON DIFFRACTIONf_bond_d0.0177017
NEUTRON DIFFRACTIONf_angle_d1.6312348
NEUTRON DIFFRACTIONf_dihedral_angle_d15.9872580
NEUTRON DIFFRACTIONf_chiral_restr0.09432
NEUTRON DIFFRACTIONf_plane_restr0.0081311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.080.1952750.14381571X-RAY DIFFRACTION43
2.08-2.17460.2398900.14992086X-RAY DIFFRACTION57
2.1746-2.2890.20271460.14742514X-RAY DIFFRACTION69
2.289-2.43220.22591630.15833009X-RAY DIFFRACTION83
2.4322-2.61960.2091560.16193470X-RAY DIFFRACTION94
2.6196-2.88240.21651690.16363466X-RAY DIFFRACTION94
2.8824-3.29780.19651490.16413485X-RAY DIFFRACTION95
3.2978-4.14830.17761750.12413503X-RAY DIFFRACTION95
4.1483-19.48950.15111840.11953572X-RAY DIFFRACTION97
2.3499-2.53090.3881020.38372125NEUTRON DIFFRACTION52
2.5309-2.78460.33191150.34822469NEUTRON DIFFRACTION60
2.7846-3.18530.27891210.28752737NEUTRON DIFFRACTION67
3.1853-4.00480.24371560.21953053NEUTRON DIFFRACTION75
4.0048-17.22340.2081680.17883246NEUTRON DIFFRACTION80
Refinement TLS params.

Method: refined / Refine-ID: NEUTRON DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.36460.74213.59851.4790.96337.82980.04260.7602-0.1686-0.24210.06060.03730.39430.83820.10980.33190.04220.04130.3555-0.00570.3711-6.6309-1.2516-0.4265
22.67320.23142.49041.38850.96917.4707-0.1327-0.57290.23580.2159-0.22370.0944-0.3813-0.7893-0.25680.34370.02230.0160.33-0.02270.365-6.53188.330829.7424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1NEUTRON DIFFRACTION1(chain 'A' and resid 1 through 182)
2NEUTRON DIFFRACTION2(chain 'B' and resid 1 through 182)

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