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- PDB-4gpc: Structure of the biliverdin-HmuO, heme oxygenase from Corynebacte... -

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Basic information

Entry
Database: PDB / ID: 4gpc
TitleStructure of the biliverdin-HmuO, heme oxygenase from Corynebacterium diphtheriae
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: 1.85 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 20, 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)75,01113
Polymers72,5103
Non-polymers2,50010
Water7,656425
1
A: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9454
Polymers24,1701
Non-polymers7753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0415
Polymers24,1701
Non-polymers8714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0254
Polymers24,1701
Non-polymers8553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.114, 63.091, 107.558
Angle α, β, γ (deg.)90.00, 100.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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)
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


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


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.56 %
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: BL44B2 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 1, 2004
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: 63266 / Num. obs: 60735 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.85→1.92 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.645 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20274 3066 5 %RANDOM
Rwork0.16838 ---
all0.17009 58115 --
obs0.17009 57650 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.207 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20.38 Å2
2--0.6 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5008 0 171 425 5604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215307
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.9887189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7755628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.53324275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06115881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7761542
X-RAY DIFFRACTIONr_chiral_restr0.220.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024120
X-RAY DIFFRACTIONr_nbd_refined0.2070.22664
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23603
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2435
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.221
X-RAY DIFFRACTIONr_mcbond_it0.9021.53214
X-RAY DIFFRACTIONr_mcangle_it1.34624971
X-RAY DIFFRACTIONr_scbond_it2.48632412
X-RAY DIFFRACTIONr_scangle_it3.8234.52218
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 215 -
Rwork0.191 4187 -
obs--99.21 %
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)
11.41150.13710.57972.17870.26251.72820.15970.0639-0.0835-0.0304-0.17550.0521-0.00830.04420.0158-0.0570.0260.0225-0.0527-0.0316-0.084423.7640.513-0.102
21.51640.558-0.14650.9420.06990.8922-0.04910.1435-0.0261-0.12250.0969-0.0021-0.0867-0.0583-0.0478-0.04260.00390.03280.01420.0175-0.07327.75216.33827.18
31.3472-0.1845-0.24690.5692-0.35820.839-0.0755-0.1854-0.02430.0923-0.0486-0.0802-0.00910.09890.1241-0.05630.00290.01850.02640.0391-0.044429.4266.08651.6
465.53077.66625.27441.678116.339118.26241.0851.4467-2.388-0.92160.4595-0.781.21370.0533-1.5444-0.0005-0.00520.00360.0018-0.00380.001424.862-9.4480.582
520.368219.521820.749527.128413.461867.9346-1.07330.86730.7683-2.39460.6166-0.4078-1.53852.2010.4566-0.00150.00090.00280.0005-0.00140.00095.77318.80417.431
617.33770.4091.61447.2385-5.056411.04160.3664-0.3097-0.0979-0.2345-0.5470.53950.5561-0.07370.1806-0.0586-0.02880.04850.01140.0522-0.04431.6660.95959.846
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 215
2X-RAY DIFFRACTION2B305 - 515
3X-RAY DIFFRACTION3C606 - 813
4X-RAY DIFFRACTION4A901
5X-RAY DIFFRACTION5B601
6X-RAY DIFFRACTION6C901

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