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- PDB-1wov: Crystal structure of heme oxygenase-2 from Synechocystis sp. PCC ... -

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Basic information

Entry
Database: PDB / ID: 1wov
TitleCrystal structure of heme oxygenase-2 from Synechocystis sp. PCC 6803 in complex with heme
ComponentsHeme oxygenase 2
KeywordsOXIDOREDUCTASE / HOMO DIMER
Function / homology
Function and homology information


heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / heme catabolic process / photosynthesis / response to oxidative stress / heme binding / 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
PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase 2
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSugishima, M. / Hagiwara, Y. / Zhang, X. / Yoshida, T. / Migita, C.T. / Fukuyama, K.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal structure of dimeric heme oxygenase-2 from Synechocystis sp. PCC 6803 in complex with heme.
Authors: Sugishima, M. / Hagiwara, Y. / Zhang, X. / Yoshida, T. / Migita, C.T. / Fukuyama, K.
History
DepositionAug 26, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2016Group: Structure summary
Revision 1.4Oct 25, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id / _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 oxygenase 2
B: Heme oxygenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3784
Polymers57,1452
Non-polymers1,2332
Water11,422634
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-58 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.163, 74.585, 72.661
Angle α, β, γ (deg.)90.00, 108.15, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer in the asymmetric unit.

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Components

#1: Protein Heme oxygenase 2


Mass: 28572.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Plasmid: pMW-A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P74133, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / 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: 2.6 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pottasium sodium tartrate, pottasium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.063 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2004
RadiationMonochromator: Si(111) Double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.063 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 53138 / Num. obs: 53138 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.75→1.84 Å / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DVE

1dve


Resolution: 1.75→19.76 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 2.76 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25374 2674 5 %RANDOM
Rwork0.19318 ---
all0.19818 50464 --
obs0.19818 50464 89.25 %-
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: 19.087 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.02 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3917 0 86 634 4637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0214115
X-RAY DIFFRACTIONr_bond_other_d0.0210.023687
X-RAY DIFFRACTIONr_angle_refined_deg1.8712.0335608
X-RAY DIFFRACTIONr_angle_other_deg1.20938565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5155482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1180.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0340.024545
X-RAY DIFFRACTIONr_gen_planes_other0.0470.02809
X-RAY DIFFRACTIONr_nbd_refined0.2840.2989
X-RAY DIFFRACTIONr_nbd_other0.2630.24379
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.22135
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2870.2442
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0410.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3380.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.1421.52431
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.02323923
X-RAY DIFFRACTIONr_scbond_it4.74631684
X-RAY DIFFRACTIONr_scangle_it6.6474.51685
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.299 201
Rwork0.22 3868

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