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- PDB-2zdp: Crystal structure of IsdI in complex with Cobalt protoporphyrin IX -

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Basic information

Entry
Database: PDB / ID: 2zdp
TitleCrystal structure of IsdI in complex with Cobalt protoporphyrin IX
ComponentsHeme-degrading monooxygenase isdI
KeywordsOXIDOREDUCTASE / ruffling / beta-barrel / cobalt protoporphyrin IX / 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 CO / Heme oxygenase (staphylobilin-producing) 2
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLee, W.C. / Reniere, M.L. / Skaar, E.P. / Murphy, M.E.P.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Ruffling of Metalloporphyrins Bound to IsdG and IsdI, Two Heme-degrading Enzymes in Staphylococcus aureus
Authors: Lee, W.C. / Reniere, M.L. / Skaar, E.P. / Murphy, M.E.P.
History
DepositionNov 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2008Provider: 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_validate_chiral / 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 / _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)27,3416
Polymers26,0312
Non-polymers1,3104
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-80 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.320, 65.668, 58.660
Angle α, β, γ (deg.)90.00, 107.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heme-degrading monooxygenase 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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7A827, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32CoN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→56 Å / Num. obs: 39272 / Observed criterion σ(F): 2 / Redundancy: 3.5 % / Rsym value: 0.045 / Net I/σ(I): 10.9
Reflection shellResolution: 1.5→1.54 Å / Rmerge(I) obs: 0.323

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XBW

1xbw


Resolution: 1.5→55.81 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.108 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2011 2079 5 %RANDOM
Rwork0.18135 ---
obs0.18233 39272 95.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.929 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20.37 Å2
2--0.32 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.5→55.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 88 267 2187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221968
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2582.0612676
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9185218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79725.636110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.4515348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.732158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021526
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2822
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21332
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2193
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.931.51122
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41721760
X-RAY DIFFRACTIONr_scbond_it1.9623973
X-RAY DIFFRACTIONr_scangle_it2.9834.5914
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 104 -
Rwork0.242 2247 -
obs--74.35 %

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