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- PDB-1we1: Crystal structure of heme oxygenase-1 from cyanobacterium Synecho... -

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Basic information

Entry
Database: PDB / ID: 1we1
TitleCrystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC6803 in complex with heme
ComponentsHeme oxygenase 1
KeywordsOXIDOREDUCTASE
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 / ISOPROPYL ALCOHOL / PHOSPHATE ION / Heme oxygenase 1
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSugishima, M. / Migita, C.T. / Zhang, X. / Yoshida, T. / Fukuyama, K.
Citation
Journal: Eur.J.Biochem. / Year: 2004
Title: Crystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC 6803 in complex with heme
Authors: Sugishima, M. / Migita, C.T. / Zhang, X. / Yoshida, T. / Fukuyama, K.
#1: Journal: Eur.J.Biochem. / Year: 2003
Title: Expression and characterization of cyanobacterium heme oxygenase, a key enzyme in the phycobilin synthesis. Properties of the heme complex of recombinant active enzyme
Authors: Migita, C.T. / Zhang, X. / Yoshida, T.
History
DepositionMay 21, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: Heme oxygenase 1
B: Heme oxygenase 1
C: Heme oxygenase 1
D: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,64923
Polymers108,3354
Non-polymers3,31419
Water3,765209
1
A: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9867
Polymers27,0841
Non-polymers9036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9516
Polymers27,0841
Non-polymers8675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8565
Polymers27,0841
Non-polymers7724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8565
Polymers27,0841
Non-polymers7724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.790, 113.730, 109.700
Angle α, β, γ (deg.)90.00, 112.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1027-

HOH

Detailsbiological unit is monomer

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Heme oxygenase 1


Mass: 27083.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Plasmid: pMW172 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P72849, heme oxygenase (biliverdin-producing)

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Non-polymers , 5 types, 228 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.9 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: PEG 400, 2-propanol, 1,5-diaminopentane dihydrochloride, sodium citrate, pottasium phosphate, pH 5.9, 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: 1.5 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 29, 2004
RadiationMonochromator: Si(111) double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 46584 / Num. obs: 46584 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 61.6 Å2 / Rsym value: 0.064 / Net I/σ(I): 7.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 5929 / Rsym value: 0.302 / % possible all: 83.2

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Processing

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

1dve


Resolution: 2.5→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 4214 -random
Rwork0.22 ---
all0.224 41943 --
obs0.224 41943 96.4 %-
Displacement parametersBiso mean: -0.079 Å2
Baniso -1Baniso -2Baniso -3
1--2.197 Å2-5.318 Å27.516 Å2
2--0 Å2-2.005 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7040 0 219 209 7468
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.214
X-RAY DIFFRACTIONc_dihedral_angle_d19.56
X-RAY DIFFRACTIONc_improper_angle_d0.752
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.427 393 -
Rwork0.348 --
obs-3913 90.7 %

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