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

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Basic information

Entry
Database: PDB / ID: 3ozw
TitleThe Crystal Structure of flavohemoglobin from R. eutrophus in complex with ketoconazole
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 / nitric oxide dioxygenase NAD(P)H activity / cellular response to nitrosative stress / nitric oxide catabolic process / FAD binding / oxygen carrier activity / response to toxic substance / oxygen binding / 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
Chem-DGG / FLAVIN-ADENINE DINUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / Chem-KKK / PHOSPHATE ION / Flavohemoprotein
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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_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.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_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_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
A: Flavohemoglobin
B: Flavohemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,36110
Polymers89,6642
Non-polymers4,6978
Water3,261181
1
A: Flavohemoglobin
hetero molecules

B: Flavohemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,36110
Polymers89,6642
Non-polymers4,6978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454-x-1/2,y+1/2,-z-1/41
Buried area7840 Å2
ΔGint-77 kcal/mol
Surface area33630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.120, 87.120, 292.160
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
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 AB

#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, 189 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-KKK / 1-acetyl-4-(4-{[(2R,4S)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine


Mass: 531.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H28Cl2N4O4 / Comment: medication, antifungal*YM
#5: 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.: 1 / Source method: obtained synthetically / Formula: C39H75O10P
#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.: 181 / 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: 60.2 %
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: 1.0007
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 12, 2008
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0007 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 47157 / % possible obs: 92 % / Observed criterion σ(I): -1 / Redundancy: 4.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.7 / % possible all: 66

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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: 2.3→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / SU B: 13.063 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2408 5.1 %RANDOM
Rwork0.205 ---
obs0.207 45024 92.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6312 0 288 181 6781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226802
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6542.0379293
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1535808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.54724.516310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.162151065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7261537
X-RAY DIFFRACTIONr_chiral_restr0.1070.2976
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215241
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
1994tight positional0.090.05
2584tight positional0.040.05
1926medium positional0.110.5
2576medium positional0.050.5
396medium positional0.140.5
1994tight thermal3.50.5
2584tight thermal7.910.5
1926medium thermal5.152
2576medium thermal9.652
396medium thermal5.292
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 130 -
Rwork0.305 2308 -
obs--65.95 %
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)
13.30561.06752.08623.4813-0.13382.38070.22770.0009-0.47790.11060.0018-0.17060.28750.1404-0.22940.28720.0316-0.1630.03590.01240.1757-25.05235.343-34.952
28.50117.6415.847914.06096.52865.44020.001-0.76950.1070.1878-0.34690.0755-0.1034-0.5770.34590.21330.0243-0.10320.1109-0.0230.1043-29.70245.396-30.879
34.8259-0.38270.69922.57760.04484.0546-0.23540.0620.30950.0481-0.0986-0.5305-0.18310.47770.33390.2796-0.0718-0.18120.11910.14440.2944-3.26148.472-23.673
46.8513-2.9451.49685.4293-2.38354.2144-0.1767-0.7287-0.08140.52440.19150.2231-0.1814-0.4029-0.01480.4293-0.0299-0.09720.32920.12770.1971-7.87135.264-4.248
53.0054-1.96491.64643.2471-1.48351.7571-0.2545-0.14570.60550.10260.0255-0.2321-0.3560.26010.2290.2738-0.0485-0.140.1708-0.0570.2411-6.46411.675-26.712
612.5173-12.70870.602316.18690.63633.29180.15610.70040.064-0.3738-0.15470.02760.21770.5659-0.00150.2277-0.0127-0.09890.17230.02380.0478-3.2493.499-34.662
73.7105-0.0890.56271.6936-0.55994.42210.23440.1202-0.33330.0006-0.0645-0.17160.37950.5603-0.16990.19540.0963-0.10730.1598-0.00280.116814.038-2.121-13.983
84.17821.95511.98316.15970.22597.43590.10160.43650.28690.12670.171-0.9648-0.56471.008-0.27260.48170.0338-0.01860.77810.12620.616727.78515.756-21.836
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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