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- PDB-1iw1: Crystal structure of a heme oxygenase (HmuO) from Corynebacterium... -

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Basic information

Entry
Database: PDB / ID: 1iw1
TitleCrystal structure of a heme oxygenase (HmuO) from Corynebacterium diphtheriae complexed with heme in the ferrous state
ComponentsHeme oxygenase
KeywordsOXIDOREDUCTASE / alpha helix / bacterial iron acquisition / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / metal ion binding
Similarity search - Function
Haem oxygenase conserved site / Heme oxygenase signature. / 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
sucrose / PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.5 Å
AuthorsHirotsu, S. / Unno, M. / Chu, G.C. / Lee, D.S. / Park, S.Y. / Shiro, Y. / Ikeda-Saito, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The crystal structures of the ferric and ferrous forms of the heme complex of HmuO, a heme oxygenase of Corynebacterium diphtheriae.
Authors: Hirotsu, S. / Chu, G.C. / Unno, M. / Lee, D.S. / Yoshida, T. / Park, S.Y. / Shiro, Y. / Ikeda-Saito, M.
History
DepositionApr 4, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heme oxygenase
B: Heme oxygenase
C: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,66317
Polymers72,5103
Non-polymers3,15214
Water10,521584
1
A: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6098
Polymers24,1701
Non-polymers1,4397
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2677
Polymers24,1701
Non-polymers1,0976
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7872
Polymers24,1701
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: Heme oxygenase
hetero molecules

B: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,87615
Polymers48,3402
Non-polymers2,53613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area5150 Å2
ΔGint-143 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.865, 62.837, 107.208
Angle α, β, γ (deg.)90.00, 101.02, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly is a monomer

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Components

#1: Protein Heme oxygenase /


Mass: 24170.158 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Plasmid: pMW172 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P71119, heme oxygenase (biliverdin-producing)
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.49 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: ammonium sulfate, NaI, MES, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 303K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
220 mMMES1droppH7.0
350 mMMES1reservoirpH5.8
42.2 Mammonium sulfate1reservoir
5230 mMsodium iodode1reservoir

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 23, 2002 / Details: mirrors
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→44 Å / Num. obs: 110939 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 4.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.306 / % possible all: 98.7
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 44 Å / Num. measured all: 651990
Reflection shell
*PLUS
% possible obs: 98.7 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: molecular replacement / Resolution: 1.5→12 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.59 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 5579 5 %RANDOM
Rwork0.177 ---
obs0.178 105106 98.89 %-
all-66791 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.027 Å2
2---0.01 Å20 Å2
3---0.026 Å2
Refinement stepCycle: LAST / Resolution: 1.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4974 0 172 380 5526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225317
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214699
X-RAY DIFFRACTIONr_angle_refined_deg1.7092.2357234
X-RAY DIFFRACTIONr_angle_other_deg0.8333.1210859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0643626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.66815891
X-RAY DIFFRACTIONr_chiral_restr0.0850.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025921
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021091
X-RAY DIFFRACTIONr_nbd_refined0.2330.31381
X-RAY DIFFRACTIONr_nbd_other0.1840.34725
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.5393
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0080.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.337
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.384
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.539
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1791.53117
X-RAY DIFFRACTIONr_mcangle_it1.90224948
X-RAY DIFFRACTIONr_scbond_it2.72432200
X-RAY DIFFRACTIONr_scangle_it4.2114.52286
X-RAY DIFFRACTIONr_rigid_bond_restr1.46825317
X-RAY DIFFRACTIONr_sphericity_free3.4532584
X-RAY DIFFRACTIONr_sphericity_bonded2.53825209
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 407
Rwork0.212 7584
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 12 Å / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.71

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