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- PDB-4g1b: X-ray structure of yeast flavohemoglobin in complex with econazole -

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Basic information

Entry
Database: PDB / ID: 4g1b
TitleX-ray structure of yeast flavohemoglobin in complex with econazole
ComponentsFlavohemoglobin
KeywordsOXIDOREDUCTASE / three domains: globin fold / antiparallel beta-barrel / alpha/beta fold / resp. / HEM / FAD / ECONAZOLE
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 binding / response to toxic substance / heme binding / metal ion binding
Similarity search - Function
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 / Globins / FAD-binding domain, ferredoxin reductase-type ...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 / Globins / 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 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-ECN / FLAVIN-ADENINE DINUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / nitric oxide dioxygenase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsEl Hammi, E. / Warkentin, E. / Demmer, U. / Baciou, L. / Ermler, U.
CitationJournal: Febs J. / Year: 2012
Title: Active site analysis of yeast flavohemoglobin based on its structure with a small ligand or econazole.
Authors: El Hammi, E. / Warkentin, E. / Demmer, U. / Marzouki, N.M. / Ermler, U. / Baciou, L.
History
DepositionJul 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Sep 13, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavohemoglobin
B: Flavohemoglobin
C: Flavohemoglobin
D: Flavohemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,00016
Polymers178,8654
Non-polymers7,13512
Water1,910106
1
A: Flavohemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5004
Polymers44,7161
Non-polymers1,7843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Flavohemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5004
Polymers44,7161
Non-polymers1,7843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Flavohemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5004
Polymers44,7161
Non-polymers1,7843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Flavohemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5004
Polymers44,7161
Non-polymers1,7843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.910, 93.830, 111.020
Angle α, β, γ (deg.)90.00, 108.22, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.978524, -0.051691, 0.199544), (0.076993, -0.989638, 0.121194), (0.191212, 0.133955, 0.972365)110.12487, 56.03636, -14.27787
3given(-0.999218, -0.028748, 0.027166), (-0.02982, 0.998757, -0.039928), (-0.025984, -0.040707, -0.998833)120.71182, 4.65891, 138.20313
4given(0.983397, -0.034107, -0.178233), (-0.039641, -0.998833, -0.027578), (-0.177084, 0.034185, -0.983602)14.17098, 75.43634, 142.77301

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Components

#1: Protein
Flavohemoglobin


Mass: 44716.230 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YJM789 / Gene: YHB1, SCY_2125 / Plasmid: pRSET 6A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A6ZUP2
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: 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.: 4 / Source method: obtained synthetically / Formula: C18H15Cl3N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 16% PEG 4000; 0.1 M Tris HCl pH 8.5 and 0.2 M lithium sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99985 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2008
RadiationMonochromator: Si(111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 37179 / Num. obs: 37179 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3→3.3 Å / % possible all: 91.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
EPMRphasing
REFMAC5.6.0095refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G1V

4g1v


Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.855 / SU B: 47.63 / SU ML: 0.429 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27992 1997 5.2 %RANDOM
Rwork0.22943 ---
all0.2321 36690 --
obs0.2321 36690 94.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.541 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å2-1.34 Å2
2--0.96 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12492 0 480 106 13078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02213310
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4842.00618092
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09351588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.22012
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029596
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: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 147 -
Rwork0.294 2690 -
obs-2690 98.95 %
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)
16.8511-0.24495.17030.25-0.99047.9034-0.40140.21380.8687-0.05490.0920.1086-0.5632-0.61390.30940.31110.0892-0.00870.2115-0.02020.476622.59325.35935.738
24.09021.5354-0.91922.77670.25236.82930.0401-0.34390.07950.1368-0.05-0.0483-0.14-0.0690.00980.0915-0.00110.01090.04030.01810.252234.2929.66157.973
34.6798-1.4425-1.97845.80320.83284.58530.08220.25960.0166-0.4874-0.0765-0.1114-0.0469-0.0072-0.00560.13390.04-0.00410.09810.09540.30645.1745.71245.335
45.3573-1.2532-5.58461.59132.00948.4025-0.090.4427-0.2496-0.2342-0.0523-0.12330.50520.63420.14230.35690.1445-0.11990.66070.17940.556792.72641.46927.338
54.74511.92031.36842.97550.07946.30990.1201-0.02850.1240.1713-0.1528-0.07580.11480.34320.03280.1431-0.0604-0.03320.13410.06140.352285.75939.60252.031
66.3538-2.58062.84796.17961.74646.2540.21590.46940.0446-0.3557-0.1753-0.10850.11920.2579-0.04070.15790.02280.07520.118-0.04210.352173.28921.35244.267
76.9767-0.63594.28650.14820.359.3935-0.3105-0.59760.652-0.01060.0987-0.0447-0.24330.14150.21170.5234-0.0783-0.03520.64760.22620.5448100.05427.53598.971
84.216-1.98790.29553.28041.36866.59140.1797-0.1417-0.05230.0105-0.0828-0.00140.23430.2608-0.09680.1967-0.0609-0.04250.21970.03990.327988.04729.87976.23
94.80250.5616-2.31244.65120.95278.15690.0461-0.78380.22870.669-0.07870.0097-0.3014-0.20330.03270.3327-0.16430.01530.4123-0.12910.466277.68847.82186.709
105.98470.4037-4.72690.9047-0.72187.550.2819-1.3691-0.25220.4286-0.14210.10050.1707-0.115-0.13990.5326-0.23070.05450.9112-0.10650.468329.30446.101105.283
114.5329-0.8939-1.06153.84441.11929.01130.359-0.13910.00210.1855-0.17170.06810.1487-0.1221-0.18720.2583-0.02120.04470.12970.03370.251336.40542.14880.99
124.69781.36751.25286.6751-1.21158.40380.1353-0.7913-0.45551.14180.0721-0.34031.35510.6064-0.20750.85420.1244-0.12520.52740.09270.576648.29724.75290.937
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 154
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2A155 - 259
4X-RAY DIFFRACTION2A402
5X-RAY DIFFRACTION3A260 - 398
6X-RAY DIFFRACTION4B6 - 154
7X-RAY DIFFRACTION4B401
8X-RAY DIFFRACTION5B155 - 259
9X-RAY DIFFRACTION5B402
10X-RAY DIFFRACTION6B260 - 398
11X-RAY DIFFRACTION7C6 - 154
12X-RAY DIFFRACTION7C401
13X-RAY DIFFRACTION8C155 - 259
14X-RAY DIFFRACTION8C402
15X-RAY DIFFRACTION9C260 - 398
16X-RAY DIFFRACTION10D6 - 154
17X-RAY DIFFRACTION10D401
18X-RAY DIFFRACTION11D155 - 259
19X-RAY DIFFRACTION11D402
20X-RAY DIFFRACTION12D260 - 398

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