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- PDB-4raj: Crystal structure of heme oxygenase 2 from Chlamydomonas reinhard... -

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Basic information

Entry
Database: PDB / ID: 4raj
TitleCrystal structure of heme oxygenase 2 from Chlamydomonas reinhardtii without heme.
ComponentsHeme oxygenase
KeywordsOXIDOREDUCTASE / Heme Oxygenase / heme / biliverdin / HMOX2
Function / homology
Function and homology information


heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / membrane => GO:0016020 / metal ion binding
Similarity search - Function
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-PG6 / Heme oxygenase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsFisher, A.J. / Lagarias, J.C.
CitationJournal: To be Published
Title: Crystal structure of heme oxygenase 2 from Chlamydomonas reinhardtii without heme.
Authors: Lopez, O. / Duanmu, D. / Lagarias, J.C. / Fisher, A.J.
History
DepositionSep 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0832
Polymers26,8161
Non-polymers2661
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.930, 134.770, 80.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

21A-565-

HOH

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Components

#1: Protein Heme oxygenase


Mass: 26816.490 Da / Num. of mol.: 1 / Fragment: UNP residues 1-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Strain: CC503 / Gene: CHLREDRAFT_152591, HMOX2 / Plasmid: pTYB12-CrHMOX2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A8JBZ0, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG Monomethyl Ether 5000, 0.2M NaCl, 0.1M Bis Tris pH 6.5. , VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2013 / Details: Si (111)
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. all: 20218 / Num. obs: 20218 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 17.45
Reflection shellResolution: 1.84→1.89 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1484 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1n45, 4g7l, 1wov, 2rgz, 1we1

1n45

4g7l

1wov

2rgz

1we1


Resolution: 1.84→35.865 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 20.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 987 4.89 %RANDOM
Rwork0.1704 ---
all0.1716 ---
obs0.1716 20198 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→35.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 18 176 1878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071739
X-RAY DIFFRACTIONf_angle_d0.9682344
X-RAY DIFFRACTIONf_dihedral_angle_d17.361636
X-RAY DIFFRACTIONf_chiral_restr0.04254
X-RAY DIFFRACTIONf_plane_restr0.005300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.93690.28631390.25182718X-RAY DIFFRACTION100
1.9369-2.05830.26441260.20032709X-RAY DIFFRACTION100
2.0583-2.21720.21491410.18162733X-RAY DIFFRACTION100
2.2172-2.44020.21651650.1722691X-RAY DIFFRACTION99
2.4402-2.79320.22511490.18432726X-RAY DIFFRACTION99
2.7932-3.51870.20831270.17662775X-RAY DIFFRACTION99
3.5187-35.87160.14681400.14562859X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00950.0249-0.01310.01850.06350.0819-0.1321-0.0068-0.23680.058-0.0311-0.38880.27770.3322-0.00640.34130.01970.12270.26960.04560.47554.955160.978436.7004
20.22950.05220.4465-0.01320.01650.37770.2045-0.2014-0.1380.0872-0.4156-0.4817-0.07980.1808-0.00150.27240.01440.00740.24340.02780.3338-1.966850.673955.4348
30.15960.20940.07810.63110.14810.14240.0456-0.0332-0.0215-0.00570.01530.16260.0459-0.185400.175-0.0047-0.00440.2292-0.030.2022-15.532646.460143.359
40.23110.3602-0.21391.13590.03120.95250.00670.0523-0.0174-0.19170.00850.0666-0.0403-0.173400.18410.0132-0.01010.2281-0.01390.1958-14.059548.976739.7269
5-0.00680.18180.06290.18290.08190.49-0.03110.1395-0.0871-0.0798-0.1127-0.4510.59610.2814-0.00360.24560.0341-0.00610.2547-0.0140.2576-3.212235.321947.2778
60.24070.15740.14660.32730.04320.13530.283-0.00410.0568-0.2819-0.0039-0.8115-0.05310.33720.05430.36640.02240.15830.233-0.04920.35330.308152.35829.3771
70.6574-0.0220.37460.77590.61650.4197-0.0108-0.1328-0.0792-0.0209-0.1081-0.2288-0.11530.069-0.00130.2070.00840.00450.1851-0.01830.2215-7.837758.695346.0196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 73 )
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 149 )
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 180 )
6X-RAY DIFFRACTION6chain 'A' and (resid 181 through 200 )
7X-RAY DIFFRACTION7chain 'A' and (resid 201 through 230 )

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