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- PDB-4wws: Structure of Chlorite dismutase-like Protein from Listeria monocy... -

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Basic information

Entry
Database: PDB / ID: 4wws
TitleStructure of Chlorite dismutase-like Protein from Listeria monocytogenes
ComponentsPutative heme-dependent peroxidase lmo2113
KeywordsOXIDOREDUCTASE / Ferredoxin-like fold / Chlorite dismutase-like protein
Function / homology
Function and homology information


hydrogen peroxide-dependent heme synthase / heme biosynthetic process / peroxidase activity / heme binding / metal ion binding
Similarity search - Function
Apc35880; domain 1 / Coproheme decarboxylase / Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Coproheme decarboxylase
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsHagmueller, A. / Mlynek, G. / Djinovic-Carugo, K.
CitationJournal: Arch.Biochem.Biophys. / Year: 2015
Title: Structure and heme-binding properties of HemQ (chlorite dismutase-like protein) from Listeria monocytogenes.
Authors: Hofbauer, S. / Hagmuller, A. / Schaffner, I. / Mlynek, G. / Krutzler, M. / Stadlmayr, G. / Pirker, K.F. / Obinger, C. / Daims, H. / Djinovic-Carugo, K. / Furtmuller, P.G.
History
DepositionNov 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 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 / pdbx_struct_conn_angle / struct_conn
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.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.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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative heme-dependent peroxidase lmo2113
B: Putative heme-dependent peroxidase lmo2113
C: Putative heme-dependent peroxidase lmo2113
D: Putative heme-dependent peroxidase lmo2113
E: Putative heme-dependent peroxidase lmo2113
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,25010
Polymers145,0545
Non-polymers1955
Water18,3751020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17460 Å2
ΔGint-38 kcal/mol
Surface area48770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.000, 128.320, 78.150
Angle α, β, γ (deg.)90.000, 105.910, 90.000
Int Tables number4
Space group name H-MP1211
DetailsOligomeric assembly in solution is hexameric as determined by the method of SEC-MALS

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Components

#1: Protein
Putative heme-dependent peroxidase lmo2113 / UPF0447 protein lmo2113


Mass: 29010.854 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo2113 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner
References: UniProt: Q8Y5F1, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1020 / 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: 2.59 Å3/Da / Density % sol: 52.56 % / Description: twin l,-k,h
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.1 M Na K tartrate, 8% glycerol, 0.1 M TrisHCl, 1/10 Silver Bullets 52: Protamine Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.26
ReflectionResolution: 2→48.76 Å / Num. obs: 99373 / % possible obs: 99.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.196 / Net I/σ(I): 6.77
Reflection shellResolution: 2→2.071 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.9392 / Mean I/σ(I) obs: 1.59 / % possible all: 99.99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
BALBESphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NN1

3nn1


Resolution: 2→48.758 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.4 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1393 1.4 %Random
Rwork0.1975 97893 --
obs0.2015 99373 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.09 Å2 / Biso mean: 27.1019 Å2 / Biso min: 11.03 Å2
Refinement stepCycle: final / Resolution: 2→48.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9760 0 5 1020 10785
Biso mean--21.83 30.31 -
Num. residues----1198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310001
X-RAY DIFFRACTIONf_angle_d0.59113511
X-RAY DIFFRACTIONf_chiral_restr0.0261418
X-RAY DIFFRACTIONf_plane_restr0.0021744
X-RAY DIFFRACTIONf_dihedral_angle_d10.8533666
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.07140.29241370.25849714985199
2.0714-2.15430.25241390.24189802994199
2.1543-2.25220.31891420.27819740988298
2.2522-2.37080.29331390.25489786992598
2.3708-2.51910.23951350.21769800993599
2.5191-2.71310.24641390.21099773991299
2.7131-2.98540.22431380.19999795993399
2.9854-3.41560.19931370.18429823996098
3.4156-4.29640.20091410.16269801994298
4.2964-20.19980.21071380.16739859999798
Refinement TLS params.Method: refined / Origin x: 89.6985 Å / Origin y: -0.2148 Å / Origin z: 23 Å
111213212223313233
T0.1882 Å2-0.0026 Å20.0233 Å2-0.048 Å2-0.0067 Å2--0.1575 Å2
L0.4169 °20.0246 °2-0.0473 °2-0.1553 °2-0.0148 °2--0.4094 °2
S0.006 Å °-0.0416 Å °0.0273 Å °0.0071 Å °-0.0073 Å °0.013 Å °0.0189 Å °0.0188 Å °0.0046 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 251
2X-RAY DIFFRACTION1allB7 - 251
3X-RAY DIFFRACTION1allC6 - 251
4X-RAY DIFFRACTION1allD7 - 251
5X-RAY DIFFRACTION1allE5 - 251
6X-RAY DIFFRACTION1allF1 - 5
7X-RAY DIFFRACTION1allS1 - 1185

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