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- PDB-1wzd: Crystal Structure Of An Artificial Metalloprotein: Fe(10-CH2CH2CO... -

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Basic information

Entry
Database: PDB / ID: 1wzd
TitleCrystal Structure Of An Artificial Metalloprotein: Fe(10-CH2CH2COOH-Salophen)/Wild Type Heme oxygenase
ComponentsHeme oxygenase
KeywordsOXIDOREDUCTASE / Electron-Transfer / Artificial Metalloprotein / Heme oxygenase
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
Chem-YOK / Heme oxygenase / heme oxygenase (biliverdin-producing)
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsUnno, M. / Yokoi, N. / Ueno, T. / Watanabe, Y. / Ikeda-Saito, M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Design of metal cofactors activated by a protein-protein electron transfer system.
Authors: Ueno, T. / Yokoi, N. / Unno, M. / Matsui, T. / Tokita, Y. / Yamada, M. / Ikeda-Saito, M. / Nakajima, H. / Watanabe, Y.
History
DepositionMar 4, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,26215
Polymers48,3402
Non-polymers1,92113
Water9,458525
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.257, 63.009, 78.159
Angle α, β, γ (deg.)90.00, 98.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heme oxygenase


Mass: 24170.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Plasmid: pMW172-A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P71119, UniProt: Q54AI1*PLUS, heme oxygenase (biliverdin-producing)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-YOK / [[2,2'-[4-CARBOXYETHYL-1,2-PHENYLENEBIS(NITRILOMETHYLIDYNE)]BIS[PHENOLATO]](2-)-N,N',O,O']-IRON / SALOPHEN-10-PROPIONATE IRON CHELATE


Mass: 442.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H18FeN2O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.08 Å3/Da / Density % sol: 40.81 %

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 92971 / Num. obs: 92971 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.35 % / Rsym value: 0.073 / Net I/σ(I): 21.9
Reflection shellResolution: 1.3→1.35 Å / % possible all: 2.28

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→29.96 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.09 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20403 8599 10.1 %RANDOM
Rwork0.17301 ---
all0.1761 ---
obs0.1761 76742 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.488 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å2-1.14 Å2
2---0.44 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.35→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 0 120 525 3934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213502
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9864738
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3455414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3423.812181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97715577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6091529
X-RAY DIFFRACTIONr_chiral_restr0.0810.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022695
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21832
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22397
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2388
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7771.52110
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20923283
X-RAY DIFFRACTIONr_scbond_it1.80631552
X-RAY DIFFRACTIONr_scangle_it2.5774.51453
X-RAY DIFFRACTIONr_rigid_bond_restr1.08933662
X-RAY DIFFRACTIONr_sphericity_free2.983525
X-RAY DIFFRACTIONr_sphericity_bonded2.34333439
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 537 -
Rwork0.198 4918 -
obs--85.27 %

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