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- PDB-1wnv: D136A mutant of Heme Oxygenase from Corynebacterium diphtheriae (HmuO) -

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Basic information

Entry
Database: PDB / ID: 1wnv
TitleD136A mutant of Heme Oxygenase from Corynebacterium diphtheriae (HmuO)
ComponentsHeme oxygenase
KeywordsOXIDOREDUCTASE / Heme / alpha-helix
Function / homology
Function and homology information


heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / heme catabolic process / response to oxidative stress / heme binding / 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
PROTOPORPHYRIN IX CONTAINING FE / Heme oxygenase
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMatsui, T. / Unno, M. / Ikeda-Saito, M.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Roles of Distal Asp in Heme Oxygenase from Corynebacterium diphtheriae, HmuO: A WATER-DRIVEN OXYGEN ACTIVATION MECHANISM
Authors: Matsui, T. / Furukawa, M. / Unno, M. / Tomita, T. / Ikeda-Saito, M.
History
DepositionAug 10, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heme oxygenase
B: Heme oxygenase
C: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,70811
Polymers72,3783
Non-polymers2,3308
Water5,549308
1
A: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8393
Polymers24,1261
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9354
Polymers24,1261
Non-polymers8093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9354
Polymers24,1261
Non-polymers8093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Heme oxygenase
hetero molecules

C: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8708
Polymers48,2522
Non-polymers1,6176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area4460 Å2
ΔGint-101 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.129, 62.781, 107.993
Angle α, β, γ (deg.)90.00, 101.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heme oxygenase


Mass: 24126.148 Da / Num. of mol.: 3 / Mutation: D136A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Plasmid: pMW172 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P71119, heme oxygenase (biliverdin-producing)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, Ammonium sulfate, sodium iodide, dioxane, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 7, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 59737 / Num. obs: 59737 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.85→1.92 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.69 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20428 6049 10.1 %RANDOM
Rwork0.16363 ---
all0.16776 53640 --
obs0.16776 53640 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.173 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20.47 Å2
2--0.62 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4964 0 154 308 5426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0215230
X-RAY DIFFRACTIONr_bond_other_d0.0040.024660
X-RAY DIFFRACTIONr_angle_refined_deg1.7772.0297109
X-RAY DIFFRACTIONr_angle_other_deg0.988310759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3765621
X-RAY DIFFRACTIONr_chiral_restr0.1160.2741
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.025862
X-RAY DIFFRACTIONr_gen_planes_other0.020.021086
X-RAY DIFFRACTIONr_nbd_refined0.2240.21236
X-RAY DIFFRACTIONr_nbd_other0.2470.25331
X-RAY DIFFRACTIONr_nbtor_other0.0870.22841
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2238
X-RAY DIFFRACTIONr_metal_ion_refined0.0820.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.29
X-RAY DIFFRACTIONr_mcbond_it1.2031.53089
X-RAY DIFFRACTIONr_mcangle_it2.15524901
X-RAY DIFFRACTIONr_scbond_it3.52632141
X-RAY DIFFRACTIONr_scangle_it5.7054.52208
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 413
Rwork0.197 3827
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)
11.21430.73311.17782.1710.29531.70120.1557-0.0280.0075-0.0111-0.0884-0.02330.03260.0237-0.06730.20370.0277-0.02210.1394-0.03390.127623.8930.569-0.193
21.22440.4529-0.07760.57260.02830.4832-0.03840.1064-0.027-0.06790.0554-0.0221-0.0508-0.0486-0.01690.1874-0.0009-0.00530.22860.01720.14667.8216.44727.329
30.789-0.1478-0.02060.169-0.47850.599-0.0889-0.1122-0.03910.0629-0.0406-0.0466-0.04110.02860.12940.18420.0059-0.00110.22540.0360.175428.976.28251.859
436.18924.755716.14671.60242.7038-6.1922-0.5080.7267-2.52130.00431.2826-1.08420.91630.482-0.77460.25410.0207-0.07280.2069-0.16960.195524.646-9.1970.775
59.81359.39561.610311.1573-0.56623.4936-0.20410.23510.0713-0.92810.0907-0.2357-0.5132-0.16280.11350.1091-0.04520.03540.15360.05390.04635.69319.07817.96
64.968-5.3547-9.0428.6306-4.320911.428-0.1483-0.1404-0.45360.45530.04630.3928-0.22170.19820.1020.0838-0.08140.03420.14020.00940.064531.0791.5860.299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 2137 - 213
2X-RAY DIFFRACTION2BB306 - 5156 - 215
3X-RAY DIFFRACTION3CC607 - 8137 - 213
4X-RAY DIFFRACTION4AI9011
5X-RAY DIFFRACTION5BJ9021
6X-RAY DIFFRACTION6CK9031

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