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- PDB-4gpf: Structure of the Fe3+-biliverdin-HmuO, heme oxygenase from Coryne... -

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Basic information

Entry
Database: PDB / ID: 4gpf
TitleStructure of the Fe3+-biliverdin-HmuO, heme oxygenase from Corynebacterium diphtheriae (data set III)
ComponentsHeme oxygenase
KeywordsOXIDOREDUCTASE / helix / heme degradation / heme
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
BILIVERDINE IX ALPHA / : / heme oxygenase (biliverdin-producing)
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsUnno, M. / Ikeda-Saito, M.
CitationJournal: To be Published
Title: Crystal Structure 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 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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_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
B: Heme oxygenase
C: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,46719
Polymers72,5103
Non-polymers2,95716
Water6,269348
1
A: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0976
Polymers24,1701
Non-polymers9275
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)25,1376
Polymers24,1701
Non-polymers9675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.937, 62.539, 107.589
Angle α, β, γ (deg.)90.00, 101.09, 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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
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: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 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: 1.9→50 Å / Num. all: 55681 / Num. obs: 54735 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.97 Å / % possible all: 89.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.144 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23877 5490 10.1 %RANDOM
Rwork0.18456 ---
all0.18995 50040 --
obs0.18995 49030 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20.59 Å2
2--0.15 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4946 0 190 348 5484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0215242
X-RAY DIFFRACTIONr_angle_refined_deg2.0462.0557107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5495621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5823.717269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89515851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5791544
X-RAY DIFFRACTIONr_chiral_restr0.1190.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024067
X-RAY DIFFRACTIONr_nbd_refined0.220.22732
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23566
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2368
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.228
X-RAY DIFFRACTIONr_mcbond_it1.0671.53169
X-RAY DIFFRACTIONr_mcangle_it1.65624903
X-RAY DIFFRACTIONr_scbond_it2.93132400
X-RAY DIFFRACTIONr_scangle_it4.4814.52204
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 340 -
Rwork0.312 3154 -
obs--85.62 %
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)
11.54450.45990.67952.04860.25771.82120.08810.0207-0.0060.0733-0.07360.02350.00030.0266-0.0145-0.05260.01780.0503-0.035-0.0081-0.069123.5980.759-0.097
21.94940.4277-0.35520.90810.01460.9163-0.05990.1332-0.0279-0.12520.0802-0.0037-0.0615-0.0745-0.0203-0.071200.05010.05650.0136-0.07127.46616.18227.302
31.7574-0.3362-0.41360.6965-0.40341.0563-0.0784-0.2193-0.04020.0888-0.0539-0.0993-0.00630.1250.1323-0.09250.00570.03970.08310.0492-0.034729.0966.0851.395
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 213
2X-RAY DIFFRACTION2B307 - 515
3X-RAY DIFFRACTION3C606 - 813

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