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- PDB-4fni: Crystal structure of IsdI-W66Y in complex with heme and cyanide -

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Basic information

Entry
Database: PDB / ID: 4fni
TitleCrystal structure of IsdI-W66Y in complex with heme and cyanide
ComponentsHeme-degrading monooxygenase isdI
KeywordsOXIDOREDUCTASE / Dimeric alpha+beta barrel
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
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase (staphylobilin-producing) 2
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsUkpabi, G.N. / Murphy, M.E.P.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Inactivation of the heme degrading enzyme IsdI by an active site substitution that diminishes heme ruffling.
Authors: Ukpabi, G. / Takayama, S.J. / Mauk, A.G. / Murphy, M.E.
History
DepositionJun 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Feb 27, 2013Group: Database references
Revision 1.3Sep 13, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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

Downloads & links

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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)27,2947
Polymers25,9852
Non-polymers1,3095
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-66 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.311, 67.014, 69.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 12992.358 Da / Num. of mol.: 2 / Mutation: W66Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: N315 / Gene: isdI, SA0160 / 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-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#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.: 338 / 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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Crystals were grown in a reservoir solution containing 25% w/v polyethylene glycol 3350, 0.2 M magnesium chloride, and 0.1 M Bis-Tris, pH 5.5, and flash frozen with a cryoprotectant of 20% ...Details: Crystals were grown in a reservoir solution containing 25% w/v polyethylene glycol 3350, 0.2 M magnesium chloride, and 0.1 M Bis-Tris, pH 5.5, and flash frozen with a cryoprotectant of 20% ethylene glycol and 20 mM sodium cyanide solution., VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 7, 2011 / Details: Varimax-VHF optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 25378 / Num. obs: 25378 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.475

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LGN

3lgn


Resolution: 1.8→25.267 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.719 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23842 1288 5.1 %RANDOM
Rwork0.19727 ---
all0.19937 24090 --
obs0.19937 24090 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.886 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.06 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 91 338 2259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0232041
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9962778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9625236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90525.424118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13915367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1651511
X-RAY DIFFRACTIONr_chiral_restr0.0760.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021609
X-RAY DIFFRACTIONr_mcbond_it0.6671.51129
X-RAY DIFFRACTIONr_mcangle_it1.25821828
X-RAY DIFFRACTIONr_scbond_it1.7533912
X-RAY DIFFRACTIONr_scangle_it2.8134.5943
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 72 -
Rwork0.243 1262 -
obs-1262 70.88 %

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