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- PDB-3ozu: The Crystal Structure of flavohemoglobin from R. eutrophus in com... -

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Basic information

Entry
Database: PDB / ID: 3ozu
TitleThe Crystal Structure of flavohemoglobin from R. eutrophus in complex with miconazole
ComponentsFlavohemoprotein
KeywordsLIPID BINDING PROTEIN / globin fold / antiparallel beta-barrel / alpha/beta fold / HEM- / FAD- / NAD- binding domains
Function / homology
Function and homology information


nitric oxide dioxygenase / nitric oxide dioxygenase NAD(P)H activity / cellular response to nitrosative stress / nitric oxide catabolic process / FAD binding / oxygen carrier activity / oxygen binding / response to toxic substance / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Flavohemoprotein / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Globin/Protoglobin / Elongation Factor Tu (Ef-tu); domain 3 / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type ...Flavohemoprotein / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Globin/Protoglobin / Elongation Factor Tu (Ef-tu); domain 3 / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Chem-X89 / Flavohemoprotein
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEl Hammi, E. / Warkentin, E. / Demmer, U. / Ermler, U. / Baciou, L.
CitationJournal: Biochemistry / Year: 2011
Title: Structure of Ralstonia eutropha Flavohemoglobin in Complex with Three Antibiotic Azole Compounds.
Authors: El Hammi, E. / Warkentin, E. / Demmer, U. / Limam, F. / Marzouki, N.M. / Ermler, U. / Baciou, L.
History
DepositionSep 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_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

Downloads & links

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Assembly

Deposited unit
A: Flavohemoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7455
Polymers44,8321
Non-polymers1,9134
Water6,053336
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Flavohemoprotein
hetero molecules

A: Flavohemoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,49010
Polymers89,6642
Non-polymers3,8268
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7480 Å2
ΔGint-93 kcal/mol
Surface area34450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.339, 105.278, 46.445
Angle α, β, γ (deg.)90.00, 101.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-446-

HOH

21A-479-

HOH

31A-710-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Flavohemoprotein / Hemoglobin-like protein / Flavohemoglobin / FHP / Nitric oxide dioxygenase / NO oxygenase / NOD


Mass: 44831.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: H16 / Gene: hmp, fhp, PHG200 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P39662, nitric oxide dioxygenase

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Non-polymers , 5 types, 340 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-X89 / 1-[(2R)-2-[(2,4-dichlorobenzyl)oxy]-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole


Mass: 416.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14Cl4N2O
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 3.24 Å3/Da / Density % sol: 61.99 %
Crystal growTemperature: 277 K / pH: 8.5
Details: 1.5M ammonium sulphate, 25% (w/v) glycerol and 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2007
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9918 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 37439 / % possible obs: 97 % / Observed criterion σ(I): -1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.9 / % possible all: 78

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
EPMRphasing
REFMAC5.6.0046refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CQX

1cqx


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.171 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1892 5 %RANDOM
Rwork0.185 ---
obs0.188 35692 98.2 %-
all-35692 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20.06 Å2
2---1.97 Å20 Å2
3---1.92 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 126 336 3619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223414
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.982.0314671
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1145412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.31324.395157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.11715543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.61520
X-RAY DIFFRACTIONr_chiral_restr0.1370.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212648
X-RAY DIFFRACTIONr_gen_planes_other
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 128 -
Rwork0.269 2414 -
obs--89.73 %
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)
12.7706-0.1794-0.67931.45370.55912.31840.0204-0.379-0.07350.2807-0.025-0.1250.05130.09990.00460.0833-0.0091-0.03340.11830.01340.043910.267428.60727.9926
27.92020.384-7.74391.9818-1.299413.00590.15930.07740.35250.0210.05350.137-0.1727-0.1846-0.21280.02260.0169-0.0170.0149-0.01560.06086.858936.0053-0.5468
32.6162-0.2602-0.62533.24250.1852.3330.03580.1426-0.1036-0.0335-0.042-0.4347-0.00130.28850.00620.0420.0196-0.02470.1042-0.02510.098831.628927.7058-8.8395
40.99131.04510.12253.33610.45730.72810.1645-0.23070.01220.3918-0.1145-0.5450.07130.222-0.050.2399-0.0306-0.07570.219300.24534.042544.76968.9668
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2A114 - 148
3X-RAY DIFFRACTION3A149 - 258
4X-RAY DIFFRACTION4A259 - 411

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