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- PDB-8uub: Structure of hypothiocyanous acid reductase (Har) from Streptococ... -

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Basic information

Entry
Database: PDB / ID: 8uub
TitleStructure of hypothiocyanous acid reductase (Har) from Streptococcus pneumoniae
ComponentsOxidoreductase, pyridine nucleotide-disulfide, class I
KeywordsOXIDOREDUCTASE / Disulphide reductase
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor / nucleotide binding
Similarity search - Function
Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / MALONATE ION / Oxidoreductase, pyridine nucleotide-disulfide, class I
Similarity search - Component
Biological speciesStreptococcus pneumoniae D39 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsShearer, H.L. / Currie, M.J. / Dickerhof, N. / Dobson, R.C.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC) New Zealand
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Hypothiocyanous acid reductase is critical for host colonization and infection by Streptococcus pneumoniae.
Authors: Shearer, H.L. / Currie, M.J. / Agnew, H.N. / Trappetti, C. / Stull, F. / Pace, P.E. / Paton, J.C. / Dobson, R.C.J. / Dickerhof, N.
History
DepositionOct 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 22, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase, pyridine nucleotide-disulfide, class I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4033
Polymers47,5161
Non-polymers8882
Water12,629701
1
A: Oxidoreductase, pyridine nucleotide-disulfide, class I
hetero molecules

A: Oxidoreductase, pyridine nucleotide-disulfide, class I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8076
Polymers95,0322
Non-polymers1,7754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area8150 Å2
ΔGint-36 kcal/mol
Surface area34460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.259, 122.259, 92.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1183-

HOH

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Components

#1: Protein Oxidoreductase, pyridine nucleotide-disulfide, class I


Mass: 47515.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae D39 (bacteria)
Strain: D39 / NCTC 7466 / Gene: SPD_1415 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2ZMK9
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.32 Å3/Da / Density % sol: 62.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2.4 M sodium malonate dibasic, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.5→47.1 Å / Num. obs: 110989 / % possible obs: 99.6 % / Redundancy: 26.6 % / CC1/2: 0.999 / Net I/σ(I): 15.2
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 4979 / CC1/2: 0.754

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MrBUMPphasing
Cootmodel building
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→47.1 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.964 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18311 5590 5 %RANDOM
Rwork0.15797 ---
obs0.15921 105305 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.041 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å2-0 Å2
2--0.08 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.5→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 60 701 4104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123760
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0281.6385171
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5095510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16424.753162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72315649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1291512
X-RAY DIFFRACTIONr_chiral_restr0.130.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022915
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.8281.8871921
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6872.8272448
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2042.1431839
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.02928.3326096
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 382 -
Rwork0.222 7283 -
obs--94.13 %

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