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- PDB-1j77: Crystal Structure of Gram-negative Bacterial Heme Oxygenase Compl... -

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Basic information

Entry
Database: PDB / ID: 1j77
TitleCrystal Structure of Gram-negative Bacterial Heme Oxygenase Complexed with Heme
ComponentsHemO
KeywordsOXIDOREDUCTASE / proximal histidine / distal helix
Function / homology
Function and homology information


heme oxidation / heme oxygenase (decyclizing) activity / metal ion binding
Similarity search - Function
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 / HemO
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsSchuller, D.J. / Zhu, W. / Stojiljkovic, I. / Wilks, A. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2001
Title: Crystal structure of heme oxygenase from the gram-negative pathogen Neisseria meningitidis and a comparison with mammalian heme oxygenase-1.
Authors: Schuller, D.J. / Zhu, W. / Stojiljkovic, I. / Wilks, A. / Poulos, T.L.
History
DepositionMay 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: HemO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2262
Polymers23,6101
Non-polymers6161
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.167, 63.167, 100.378
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

Detailsthe enzyme is a monomer

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Components

#1: Protein HemO / heme oxygenase


Mass: 23609.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: hemO / Plasmid: pWMZ1651 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9RGD9, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.12 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 3350, sodium acetate, Tris hydrochloride, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-HCl1reservoir
20.2 Msodium acetate1reservoir
332.5 %PEG33501reservoir
432 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.5498, 1.7377, 1.7401, 1.9075
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 26, 2000
Details: Flat mirror(vertical) single crystal (Si311) bent monochromator (horizontal)
RadiationMonochromator: bent crystal Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54981
21.73771
31.74011
41.90751
ReflectionResolution: 1.5→44.67 Å / Num. all: 31486 / Num. obs: 31486 / % possible obs: 0.946 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 23.743 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 13.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1381 / % possible all: 92.1
Reflection
*PLUS
% possible obs: 94.9 % / Num. measured all: 161249
Reflection shell
*PLUS
% possible obs: 92.1 %

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→53.45 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: REFMAC5 / Details: Maximum likelihood based on F
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1605 5.1 %RANDOM
Rwork0.227 ---
all0.2289 29881 --
obs0.2289 29881 94.61 %-
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.102 Å0.134 Å
Luzzati sigma a-0.097 Å
Refinement stepCycle: LAST / Resolution: 1.5→53.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1588 0 48 244 1880
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0171.437
X-RAY DIFFRACTIONp_angle_d1.5432.133
X-RAY DIFFRACTIONp_torsion1_d3.42.664
X-RAY DIFFRACTIONp_torsion3_d15.83.835
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: -0
RfactorNum. reflection% reflection
Rfree0.281 107 -
Rwork0.238 --
obs-2212 93 %
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.5432.133
X-RAY DIFFRACTIONp_chiral_restr0.099

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