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- PDB-3lgn: Crystal structure of IsdI in complex with heme -

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Basic information

Entry
Database: PDB / ID: 3lgn
TitleCrystal structure of IsdI in complex with heme
ComponentsHeme-degrading monooxygenase isdI
KeywordsOXIDOREDUCTASE / Dimeric alpha+beta barrel / Cytoplasm / Heme / Iron / Metal-binding / Monooxygenase
Function / homology
Function and homology information


heme oxygenase (staphylobilin-producing) / iron import into cell / heme oxygenase (decyclizing) activity / heme catabolic process / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Heme oxygenase IsdG / : / ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Heme oxygenase (staphylobilin-producing) 2
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsUkpabi, G.N. / Murphy, M.E.P.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: The IsdG-family of haem oxygenases degrades haem to a novel chromophore
Authors: Reniere, M.L. / Ukpabi, G.N. / Harry, S.R. / Stec, D.F. / Krull, R. / Wright, D.W. / Bachmann, B.O. / Murphy, M.E.P. / Skaar, E.P.
History
DepositionJan 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq_dif / struct_site
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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme-degrading monooxygenase isdI
B: Heme-degrading monooxygenase isdI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3527
Polymers26,0312
Non-polymers1,3215
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-15 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.240, 66.780, 69.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heme-degrading monooxygenase isdI / IsdI / Iron-regulated surface determinant isdI / Iron-responsive surface determinant isdI / Heme oxygenase


Mass: 13015.394 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: IsdI / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)
References: UniProt: Q7A827, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMAGNESIUM ION 600 IS COORDINATED BY 6 WATERS 601-606.

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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: 52.57 % / Mosaicity: 1.01 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% polyethylene glycol 3350, 0.2M MgCl2, 0.1M Bis-Tris buffer pH 5.5, and flash frozen with a cryoprotectant of 10% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2008
Details: DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror.
RadiationMonochromator: double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.5→69.43 Å / Num. all: 43991 / Num. obs: 43991 / % possible obs: 99.8 % / Redundancy: 6.8 % / Rsym value: 0.077

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZDP

2zdp


Resolution: 1.5→44.62 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.189 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.878 / SU B: 2.958 / SU ML: 0.05 / SU R Cruickshank DPI: 0.09 / SU Rfree: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2217 5 %RANDOM
Rwork0.181 ---
all0.213 44056 --
obs0.183 43931 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 245.04 Å2 / Biso mean: 21.709 Å2 / Biso min: 8.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å20 Å2
2--0.33 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 91 281 2256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222034
X-RAY DIFFRACTIONr_angle_refined_deg1.1182.0642779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8795229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61925.517116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33715359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8291510
X-RAY DIFFRACTIONr_chiral_restr0.0710.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021604
X-RAY DIFFRACTIONr_mcbond_it0.7591.51123
X-RAY DIFFRACTIONr_mcangle_it1.36821823
X-RAY DIFFRACTIONr_scbond_it1.9393911
X-RAY DIFFRACTIONr_scangle_it2.974.5956
X-RAY DIFFRACTIONr_rigid_bond_restr0.93532034
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 170 -
Rwork0.259 3051 -
all-3221 -
obs-3222 99.97 %

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