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- PDB-1p3t: Crystal Structures of the NO-and CO-Bound Heme Oxygenase From Nei... -

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Basic information

Entry
Database: PDB / ID: 1p3t
TitleCrystal Structures of the NO-and CO-Bound Heme Oxygenase From Neisseria Meningitidis: Implications for Oxygen Activation
ComponentsHeme oxygenase 1
KeywordsOXIDOREDUCTASE / heme oxygenase / heme degradation
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFriedman, J. / Lad, L. / Deshmukh, R. / Li, H. / Wilks, A. / Poulos, T.L.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structures of the NO- and CO-bound heme oxygenase from Neisseriae meningitidis. Implications for O2 activation
Authors: Friedman, J. / Lad, L. / Deshmukh, R. / Li, H. / Wilks, A. / Poulos, T.L.
History
DepositionApr 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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: Heme oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2262
Polymers23,6101
Non-polymers6161
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.245, 63.245, 102.142
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein Heme oxygenase 1 / E.C.1.14.99.3 / HO-1 / heme oxygenase (decyclizing) 1


Mass: 23609.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Heme-complexed / 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.: 62 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: tris-HCl, sodium acetate, PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MTris-HCl1reservoirpH8.5
20.2 Msodium acetate1reservoir
332.5 %PEG33501reservoir
423 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 119 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 14, 2002 / Details: mirrors
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 12602 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Rmerge(I) obs: 0.051 / Rsym value: 0.067 / Net I/σ(I): 38.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.67 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.37 / Num. unique all: 1284 / Rsym value: 0.555 / % possible all: 97.8
Reflection
*PLUS
Num. obs: 31166 / % possible obs: 96.7 % / Num. measured all: 226194
Reflection shell
*PLUS
% possible obs: 97.8 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J77

1j77


Resolution: 2.1→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 609 4.8 %random
Rwork0.254 ---
all-12602 --
obs-12602 94.6 %-
Displacement parametersBiso mean: 46.44 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 43 62 1684
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.37
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.374

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