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- PDB-4gph: Structure of HmuO, heme oxygenase from Corynebacterium diphtheria... -

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Basic information

Entry
Database: PDB / ID: 4gph
TitleStructure of HmuO, heme oxygenase from Corynebacterium diphtheriae, in complex with the putative reaction intermediates between Fe3+-biliverdin and biliverdin (data set IV)
ComponentsHeme oxygenase
KeywordsOXIDOREDUCTASE / helix / heme degradation / heme
Function / homology
Function and homology information


heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / 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
ASCORBIC ACID / BILIVERDINE IX ALPHA / : / heme oxygenase (biliverdin-producing)
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsUnno, M. / Ikeda-Saito, M.
CitationJournal: To be Published
Title: Crystal Structures of the Substrate-Free and the Product-Bound forms of HmuO, a Heme Oxygenase from Corynebacterium diphtheriae
Authors: Unno, M. / Ardevol, A. / Rovira, C. / Ikeda-Saito, M.
History
DepositionAug 21, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)75,31517
Polymers72,5103
Non-polymers2,80414
Water8,521473
1
A: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9054
Polymers24,1701
Non-polymers7353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2337
Polymers24,1701
Non-polymers1,0636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1776
Polymers24,1701
Non-polymers1,0075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.065, 62.966, 107.728
Angle α, β, γ (deg.)90.00, 100.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules ABC

#1: Protein Heme oxygenase /


Mass: 24170.158 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q54AI1, heme oxygenase (biliverdin-producing)
#5: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: medication*YM

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Non-polymers , 4 types, 486 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H34N4O6
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 303 K / Method: vapor diffusion / pH: 6.1
Details: ammonium sulfate, MES, pH 6.1, VAPOR DIFFUSION, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 20, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 78377 / Num. obs: 77319 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.76 Å / % possible all: 95.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.953 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20547 7805 10.1 %RANDOM
Rwork0.16521 ---
all0.16934 70408 --
obs0.16934 69486 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.928 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20.37 Å2
2--0.73 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4961 0 183 473 5617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0215361
X-RAY DIFFRACTIONr_angle_refined_deg2.3362.0967281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3525627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47623.764271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2515848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3321544
X-RAY DIFFRACTIONr_chiral_restr0.1710.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0270.0224186
X-RAY DIFFRACTIONr_mcbond_it1.3881.53122
X-RAY DIFFRACTIONr_mcangle_it2.25824949
X-RAY DIFFRACTIONr_scbond_it3.59132239
X-RAY DIFFRACTIONr_scangle_it5.5534.52332
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 538 -
Rwork0.277 4899 -
obs--94.59 %
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)
11.51820.22320.63782.38410.28421.6940.16460.0381-0.0992-0.0414-0.16840.01120.00090.04590.00390.05330.01660.00280.0559-0.02030.029723.8680.7260.026
21.39770.474-0.11530.90280.04520.8966-0.04790.1461-0.0511-0.12190.0834-0.0246-0.072-0.0487-0.03540.03520.00440.01760.08990.01220.01477.84116.06727.677
31.1786-0.2222-0.20250.5187-0.29880.6586-0.0765-0.1377-0.02190.0793-0.0266-0.0736-0.01340.08930.10320.02420.00340.00540.09710.03030.037629.7485.82851.426
471.2262-0.144215.372322.52692.879949.7772.10742.5101-4.362-0.515-0.4962-0.01132.8875-0.224-1.61130.31140.0286-0.130.1173-0.16870.381724.788-9.4730.846
550.932639.8138-2.522231.2219-2.13482.9628-2.09662.3321.5641-1.53491.19361.1431-1.28092.47510.9031.2145-0.9605-0.56633.05610.82681.45445.75119.00717.516
615.93631.59360.58455.0825-8.129813.7479-0.0379-0.34340.4204-0.1782-0.02410.09210.4412-0.11410.06190.2221-0.11990.18060.2167-0.03520.207931.5460.94759.898
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 213
2X-RAY DIFFRACTION2B307 - 514
3X-RAY DIFFRACTION3C603 - 813
4X-RAY DIFFRACTION4A3002
5X-RAY DIFFRACTION5B601
6X-RAY DIFFRACTION6C902

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