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- PDB-1p3v: Crystal Structures of the NO-and CO-Bound Heme Oxygenase From Nei... -

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Basic information

Entry
Database: PDB / ID: 1p3v
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / HemO
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 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 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2543
Polymers23,6101
Non-polymers6442
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.449, 60.449, 102.361
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-452-

HOH

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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: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.98 Å3/Da / Density % sol: 37.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris-HCl, sodium acetate, PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
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: Aug 2, 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: 2.25→50 Å / Num. all: 9526 / Num. obs: 9467 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Rmerge(I) obs: 0.054 / Rsym value: 0.064 / Net I/σ(I): 21.3
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.39 / Num. unique all: 924 / Rsym value: 0.599 / % possible all: 89.8
Reflection
*PLUS
Num. obs: 26432 / % possible obs: 89.7 % / Num. measured all: 123533
Reflection shell
*PLUS
% possible obs: 89.8 % / Rmerge(I) obs: 0.54

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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: 2.25→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 505 5.3 %random
Rwork0.249 ---
all-9526 --
obs-9467 94.1 %-
Displacement parametersBiso mean: 50.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1578 0 45 52 1675
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.402
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
2.25-2.330.3409470.31578779.26
2.33-2.420.2771510.30248709.19
2.42-2.530.3437330.30848909.4
2.53-2.670.3358500.30468809.28
2.67-2.830.3276530.29098799.28
2.83-3.050.2628470.25649049.55
3.05-3.360.3294490.27388969.46
3.36-3.850.2724600.24518979.48
3.85-4.850.2676570.20869179.68
4.85-500.3004580.23495210.05
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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