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- PDB-1wnw: D136N mutant of Heme Oxygenase from Corynebacterium diphtheriae (HmuO) -

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Basic information

Entry
Database: PDB / ID: 1wnw
TitleD136N 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 / IODIDE ION / Heme oxygenase
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsUnno, M. / Matsui, T. / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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

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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)76,69829
Polymers72,5083
Non-polymers4,19026
Water6,882382
1
A: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5819
Polymers24,1691
Non-polymers1,4128
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,82013
Polymers24,1691
Non-polymers1,65012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2977
Polymers24,1691
Non-polymers1,1286
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)51,11620
Polymers48,3382
Non-polymers2,77818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area6160 Å2
ΔGint-181 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.059, 63.101, 107.164
Angle α, β, γ (deg.)90.00, 101.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Heme oxygenase


Mass: 24169.172 Da / Num. of mol.: 3 / Mutation: D136N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Plasmid: PMW172 / Production host: Escherichia coli (E. coli)
References: UniProt: P71119, heme oxygenase (biliverdin-producing)

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Non-polymers , 5 types, 408 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, Glycerol, Sodium iodide, Ammonium Sulfate, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 75503 / Num. obs: 75503 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.76 Å / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.51 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23347 7615 10.1 %RANDOM
Rwork0.19576 ---
all0.19863 ---
obs0.19863 67872 97.18 %-
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: 15.716 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20.37 Å2
2--1.27 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4956 0 200 382 5538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0215250
X-RAY DIFFRACTIONr_bond_other_d0.0050.024642
X-RAY DIFFRACTIONr_angle_refined_deg1.9262.0337143
X-RAY DIFFRACTIONr_angle_other_deg1.263310703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7545621
X-RAY DIFFRACTIONr_chiral_restr0.1290.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025872
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021094
X-RAY DIFFRACTIONr_nbd_refined0.230.21372
X-RAY DIFFRACTIONr_nbd_other0.2520.25562
X-RAY DIFFRACTIONr_nbtor_other0.0890.22917
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2292
X-RAY DIFFRACTIONr_metal_ion_refined0.170.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.221
X-RAY DIFFRACTIONr_mcbond_it1.3091.53090
X-RAY DIFFRACTIONr_mcangle_it2.12324897
X-RAY DIFFRACTIONr_scbond_it3.35132160
X-RAY DIFFRACTIONr_scangle_it5.1114.52246
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.281 498
Rwork0.23 4817
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)
13.16540.14782.16981.31470.89863.0259-0.0162-0.0416-0.080.2890.01690.06840.2738-0.157-0.00070.31170.0062-0.04550.0547-0.01710.154619.421-9.932.053
20.95160.66020.611.89341.29962.1911-0.04130.08950.1429-0.06390.04130.1203-0.09970.0517-0.00010.25570.0004-0.00290.09580.00760.167822.6994.445-3.446
31.05320.25780.00442.03740.81721.78980.10480.0173-0.11620.32070.0935-0.1040.21340.2256-0.19830.26950.0515-0.02570.0821-0.03010.122230.161-2.0244.885
43.83432.58460.41562.95350.5784-0.054-0.12620.17470.3594-0.32650.10140.2775-0.1241-0.090.02470.23680.01480.01850.21130.08910.13285.04124.55219.331
51.77090.5691-0.38580.6366-0.14890.86680.053-0.0178-0.0301-0.0301-0.0295-0.022-0.0387-0.0097-0.02350.21540.00860.03010.17760.02250.166111.47915.37430.365
62.21550.7383-0.29321.4491-0.21450.908-0.06850.2998-0.0787-0.090.07910.1414-0.0062-0.1305-0.01060.17740.00850.00880.20060.01990.11340.98712.17123.454
76.9284-4.8293-3.00111.43981.20645.8463-0.582-0.7255-0.57580.47230.09190.10670.10470.10620.49010.1622-0.06850.03410.19240.08830.160932.2136.37562.275
82.1581-0.1934-0.12270.8125-0.35831.0746-0.0451-0.5788-0.23380.078-0.0819-0.0665-0.04810.18610.12690.1457-0.00520.02040.32150.12040.146825.3888.19848.432
92.07550.2458-0.57211.7392-0.55251.006-0.1237-0.3041-0.32620.1462-0.0046-0.1073-0.01150.08450.12830.15440.01590.01040.25070.15870.100536.2850.89751.276
10-0.55942.2688.0653.75961.152911.77470.01790.16920.0312-0.15150.0676-0.18160.99640.2348-0.08550.37040.0501-0.05130.13-0.05990.215325.026-9.1710.406
1113.36895.61771.13167.31012.30325.018-0.05450.69580.3643-0.38660.11320.0807-0.10890.0284-0.05860.23040.01220.02890.23690.06820.15325.67718.88117.812
1217.7673-13.88942.702320.9106-1.01415.9606-0.3905-1.18440.18761.4183-0.4435-0.46640.07870.3160.83390.2415-0.00450.1020.22540.08390.116431.3691.61960.09
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 397 - 39
2X-RAY DIFFRACTION2AA40 - 16040 - 160
3X-RAY DIFFRACTION3AA161 - 212161 - 212
4X-RAY DIFFRACTION4BB7 - 397 - 39
5X-RAY DIFFRACTION5BB40 - 16040 - 160
6X-RAY DIFFRACTION6BB161 - 212161 - 212
7X-RAY DIFFRACTION7CC7 - 397 - 39
8X-RAY DIFFRACTION8CC40 - 16040 - 160
9X-RAY DIFFRACTION9CC161 - 212161 - 212
10X-RAY DIFFRACTION10AAA9011
11X-RAY DIFFRACTION11BBA9021
12X-RAY DIFFRACTION12CCA9031

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