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- PDB-4oz5: Bacillus subtilis HmoB -

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Basic information

Entry
Database: PDB / ID: 4oz5
TitleBacillus subtilis HmoB
ComponentsBacillus subtilis HmoB
KeywordsOXIDOREDUCTASE / Heme monooxygenase
Function / homology
Function and homology information


heme oxygenase (biliverdin-producing) / heme oxygenase (decyclizing) activity / metal ion binding / cytoplasm
Similarity search - Function
: / ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / : / Heme-degrading monooxygenase HmoB
Similarity search - Component
Biological speciesBacillus subtilis subsp. spizizenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.71 Å
AuthorsChoe, J. / Park, S.
CitationJournal: To Be Published
Title: Bacillus subtilis HmoB
Authors: Choe, J.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_related / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_keywords / symmetry
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_related.content_type / _pdbx_database_related.details / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_keywords.text / _symmetry.Int_Tables_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacillus subtilis HmoB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4342
Polymers17,8171
Non-polymers6161
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-19 kcal/mol
Surface area8520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.597, 99.597, 99.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-343-

HOH

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Components

#1: Protein Bacillus subtilis HmoB


Mass: 17817.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. spizizenii (bacteria)
Strain: ATCC 6633 / Gene: BSU6633_15062 / Production host: Escherichia coli (E. coli) / References: UniProt: D5N3U6, UniProt: P38049*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.3 M Sodium Citrate, 0.5% PEG 2000, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 4635 / % possible obs: 100 % / Redundancy: 25 % / Net I/σ(I): 45.6

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementResolution: 2.71→19.53 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.891 / SU B: 31.988 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27138 214 4.7 %RANDOM
Rwork0.19323 ---
obs0.19673 4381 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.81 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.71→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 43 49 1351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191339
X-RAY DIFFRACTIONr_bond_other_d0.0070.021247
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9871828
X-RAY DIFFRACTIONr_angle_other_deg0.78332863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3395153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17124.61565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.21515221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.08156
X-RAY DIFFRACTIONr_chiral_restr0.0920.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211515
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02325
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.707→2.776 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 18 -
Rwork0.222 296 -
obs--99.37 %
Refinement TLS params.Method: refined / Origin x: 1.2547 Å / Origin y: 19.241 Å / Origin z: 29.4051 Å
111213212223313233
T0.207 Å20.0367 Å20.0878 Å2-0.4936 Å2-0.0188 Å2--0.213 Å2
L9.0886 °22.4548 °20.7951 °2-9.4877 °2-2.497 °2--5.2893 °2
S0.1314 Å °-1.4749 Å °0.1952 Å °0.8549 Å °0.229 Å °1.138 Å °-0.0597 Å °-0.5894 Å °-0.3604 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 166
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION1A301 - 349

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