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- PDB-5kzl: Structure of Heme Oxygenase from Leptospira interrogans -

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Basic information

Entry
Database: PDB / ID: 5kzl
TitleStructure of Heme Oxygenase from Leptospira interrogans
ComponentsHeme oxygenase
KeywordsOXIDOREDUCTASE / Heme oxygenase Leptospira
Function / homology
Function and homology information


: / heme oxidation / heme oxygenase (decyclizing) activity / heme catabolic process / response to oxidative stress / heme binding / metal ion binding
Similarity search - Function
Haem oxygenase / Haem oxygenase-like / Heme oxygenase / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / : / Heme oxygenase
Similarity search - Component
Biological speciesLeptospira interrogans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsKlinke, S. / Soldano, A. / Otero, L.H. / Rivera, M. / Catalano-Dupuy, D.L. / Ceccarelli, E.A.
Funding support Argentina, United States, 4items
OrganizationGrant numberCountry
ANPCyTPICT 2012-1841 Argentina
National Scientific and Technical Research Council (CONICET)PIP 112-201201-00345-CO Argentina
National Scientific and Technical Research Council (CONICET)CONICET-NSF 993/13, Bio187 Argentina
National Science Foundation (NSF, United States)MCB 1158469 United States
CitationJournal: PLoS ONE / Year: 2017
Title: Structural and mutational analyses of the Leptospira interrogans virulence-related heme oxygenase provide insights into its catalytic mechanism.
Authors: Soldano, A. / Klinke, S. / Otero, L.H. / Rivera, M. / Catalano-Dupuy, D.L. / Ceccarelli, E.A.
History
DepositionJul 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8512
Polymers24,2341
Non-polymers6161
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.640, 58.790, 86.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMonomer according to electrophoresis in non-denaturing polyacrylamide gels

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Components

#1: Protein Heme oxygenase


Mass: 24234.412 Da / Num. of mol.: 1 / Mutation: C26S
Source method: isolated from a genetically manipulated source
Details: The complete Heme Oxygenase protein has 20 extra residues at its C-terminus, which were not present in the construct used for crystallization. Additionally, the construct used for ...Details: The complete Heme Oxygenase protein has 20 extra residues at its C-terminus, which were not present in the construct used for crystallization. Additionally, the construct used for crystallization bear also a 7-residue cloning artifact at the N-terminus (GHMASGS) and a point mutation with respect to the wild-type protein (C26S).
Source: (gene. exp.) Leptospira interrogans (bacteria) / Gene: hol, LA733_3616 / Plasmid: pET-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A109I1W7, UniProt: Q8EXM2*PLUS, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 1.98 Å3/Da / Density % sol: 38 % / Description: Thin dark orange plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 24% PEG 4000 0,1 M sodium citrate (pH 6.0) 0,2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.5418 Å
DetectorType: BRUKER PHOTON 100 / Detector: PIXEL / Date: Sep 30, 2014 / Details: HELIOS MX MULTILAYER OPTICS
RadiationMonochromator: HELIOS MX MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→31.7 Å / Num. obs: 20079 / % possible obs: 96.7 % / Redundancy: 13.2 % / Biso Wilson estimate: 16.82 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Net I/σ(I): 20.8
Reflection shellResolution: 1.73→1.83 Å / Redundancy: 10 % / Rmerge(I) obs: 1.178 / Mean I/σ(I) obs: 2.64 / CC1/2: 0.613 / % possible all: 89.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
Cootmodel building
PROTEUM PLUSPROTEUM2 from Brukerdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WE1

1we1


Resolution: 1.73→31.7 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.144 / SU Rfree Blow DPI: 0.128 / SU Rfree Cruickshank DPI: 0.122
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1004 5 %RANDOM
Rwork0.184 ---
obs0.186 20079 96.7 %-
Displacement parametersBiso mean: 16.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.1792 Å20 Å20 Å2
2--2.5344 Å20 Å2
3----1.3552 Å2
Refinement stepCycle: 1 / Resolution: 1.73→31.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 43 219 1928
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011826HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.992496HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d628SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes281HARMONIC5
X-RAY DIFFRACTIONt_it1826HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion18.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion217SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2357SEMIHARMONIC4
LS refinement shellResolution: 1.73→1.82 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3226 130 4.98 %
Rwork0.2929 2483 -
all0.2944 2613 -
obs--88.32 %

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