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

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Basic information

Entry
Database: PDB / ID: 3ozv
TitleThe Crystal Structure of flavohemoglobin from R. eutrophus in complex with econazole
ComponentsFlavohemoglobin
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 / cellular response to nitrosative stress / nitric oxide dioxygenase [NAD(P)H] activity / 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 / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Globin/Protoglobin / Elongation Factor Tu (Ef-tu); domain 3 / Globins / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / Globin-like ...Flavohemoprotein / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Globin/Protoglobin / Elongation Factor Tu (Ef-tu); domain 3 / Globins / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / Globin-like / 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 / Globin / Globin / Globin domain profile. / Globin-like superfamily / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-DGG / Chem-ECN / FLAVIN-ADENINE DINUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Flavohemoprotein
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
B: Flavohemoglobin
A: Flavohemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,79611
Polymers89,6642
Non-polymers5,1329
Water2,180121
1
A: Flavohemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4466
Polymers44,8321
Non-polymers2,6145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flavohemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3515
Polymers44,8321
Non-polymers2,5194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Flavohemoglobin
hetero molecules

B: Flavohemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,79611
Polymers89,6642
Non-polymers5,1329
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454-x-1/2,y+1/2,-z-1/41
Buried area7610 Å2
ΔGint-77 kcal/mol
Surface area34290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.220, 87.220, 291.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
12A
22B
13A
23B
/ NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules BA

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


Mass: 44831.871 Da / Num. of mol.: 2
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 , 6 types, 130 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-DGG / 1-[GLYCEROLYLPHOSPHONYL]-2-[8-(2-HEXYL-CYCLOPROPYL)-OCTANAL-1-YL]-3-[HEXADECANAL-1-YL]-GLYCEROL


Mass: 734.981 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H75O10P
#5: Chemical ChemComp-ECN / 1-[(2S)-2-[(4-CHLOROBENZYL)OXY]-2-(2,4-DICHLOROPHENYL)ETHYL]-1H-IMIDAZOLE / S-Econazole


Mass: 381.684 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H15Cl3N2O
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.09 Å3/Da / Density % sol: 60.17 %
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: Jul 6, 2008
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9918 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 43225 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.97 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.7
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.4 / % possible all: 86.3

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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: 2.4→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 15.869 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2263 5.1 %RANDOM
Rwork0.21 ---
obs0.212 42490 99 %-
all-42490 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6312 0 283 121 6716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226785
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.582.0359263
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.26524.563309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.763151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.391536
X-RAY DIFFRACTIONr_chiral_restr0.1050.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215228
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1995medium positional0.250.5
2655medium positional0.340.5
368medium positional0.370.5
1933loose positional0.425
2507loose positional0.615
369loose positional0.415
1995medium thermal2.092
2655medium thermal10.082
368medium thermal5.462
1933loose thermal3.1410
2507loose thermal7.5110
369loose thermal4.3910
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 160 -
Rwork0.343 2959 -
obs--95.65 %
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)
14.79332.12.44954.44730.0132.20980.3764-0.1629-0.73670.1063-0.0114-0.21760.35510.0803-0.36490.2990.0205-0.20210.05840.0450.2368-25.13535.355-34.757
29.37277.77154.942317.96055.71682.9615-0.081-1.46790.0621-0.2506-0.16810.4333-0.2103-0.6930.24910.16660.0761-0.17320.3618-0.05350.2019-29.66245.5-30.787
35.3512-0.90970.61772.76540.4534.5344-0.1454-0.12610.36040.0669-0.1169-0.6445-0.06960.4440.26230.2299-0.0514-0.15250.08360.11050.3138-3.06848.31-23.959
48.119-4.40292.06957.5705-2.49925.0583-0.1077-0.88360.0450.7895-0.0066-0.0284-0.1123-0.35150.11430.4286-0.104-0.12640.3290.13530.192-7.58835.136-4.424
53.7624-2.47022.00764.3934-1.99422.9672-0.2267-0.03620.6460.2919-0.001-0.2725-0.33020.44260.22770.2253-0.0485-0.15330.1207-0.02620.2138-6.35711.632-26.612
611.703-13.68540.731918.69730.33124.70530.40730.7512-0.0694-0.4325-0.16910.10730.23360.7938-0.23820.19790.0283-0.11330.2855-0.00720.074-3.2233.539-34.581
75.0035-0.65910.59782.2487-0.74195.90490.33580.1964-0.38550.1488-0.1269-0.24030.41080.7783-0.20880.25640.092-0.17130.1449-0.01260.180314.208-2.087-14.008
84.64692.59853.05028.34811.283410.6585-0.07430.64540.48470.48370.2988-1.5393-0.45511.5571-0.22460.58170.0319-0.08881.06780.10390.980727.78716.123-21.679
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 - 392
5X-RAY DIFFRACTION5B1 - 113
6X-RAY DIFFRACTION6B114 - 148
7X-RAY DIFFRACTION7B149 - 258
8X-RAY DIFFRACTION8B259 - 392

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