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- PDB-2ivf: Ethylbenzene dehydrogenase from Aromatoleum aromaticum -

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Basic information

Entry
Database: PDB / ID: 2ivf
TitleEthylbenzene dehydrogenase from Aromatoleum aromaticum
Components(ETHYLBENZENE DEHYDROGENASE ...) x 3
KeywordsOXIDOREDUCTASE / ANAEROBIC HYDROCARBON DEGRADATION / MOCO / FE/S CLUSTER / MO- BISMGD ENZYME / DMSO REDUCTASE FAMILY
Function / homology
Function and homology information


molybdopterin cofactor binding / cell envelope / anaerobic respiration / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / oxidoreductase activity / heme binding / metal ion binding / membrane
Similarity search - Function
Ethylbenzene dehydrogenase / DMSO reductase family, type II, haem b-binding subunit / Cytochrome c-552/DMSO reductase-like, haem-binding domain / Ethylbenzene dehydrogenase / DMSO reductase family, type II, iron-sulphur subunit / DMSO reductase family, type II, molybdopterin subunit / Immunoglobulin-like - #1190 / : / 4Fe-4S dicluster domain / Molybdopterin dinucleotide-binding domain ...Ethylbenzene dehydrogenase / DMSO reductase family, type II, haem b-binding subunit / Cytochrome c-552/DMSO reductase-like, haem-binding domain / Ethylbenzene dehydrogenase / DMSO reductase family, type II, iron-sulphur subunit / DMSO reductase family, type II, molybdopterin subunit / Immunoglobulin-like - #1190 / : / 4Fe-4S dicluster domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / FE3-S4 CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-MD1 / Chem-MGD / MOLYBDENUM ATOM / PHOSPHATE ION / IRON/SULFUR CLUSTER / Alpha-subunit of ethylbenzene dehydrogenase / Beta-subunit of ethylbenzene dehydrogenase / Gamma-subunit of ethylbenzene dehydrogenase
Similarity search - Component
Biological speciesAROMATOLEUM AROMATICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsKloer, D.P. / Hagel, C. / Heider, J. / Schulz, G.E.
CitationJournal: Structure / Year: 2006
Title: Crystal Structure of Ethylbenzene Dehydrogenase from Aromatoleum Aromaticum
Authors: Kloer, D.P. / Hagel, C. / Heider, J. / Schulz, G.E.
History
DepositionJun 13, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.ptnr2_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT
B: ETHYLBENZENE DEHYDROGENASE BETA-SUBUNIT
C: ETHYLBENZENE DEHYDROGENASE GAMMA-SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,27424
Polymers173,2333
Non-polymers5,04121
Water14,736818
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19390 Å2
ΔGint-195.6 kcal/mol
Surface area44280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.532, 67.324, 114.765
Angle α, β, γ (deg.)90.00, 111.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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ETHYLBENZENE DEHYDROGENASE ... , 3 types, 3 molecules ABC

#1: Protein ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT


Mass: 110402.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: AZOARCUS SP. EBN1 RENAMED TO AROMATOLEUM AROMATICUM
Source: (natural) AROMATOLEUM AROMATICUM (bacteria) / Strain: EBN1 / References: UniProt: Q5P5I0, EC: 1.17.99.2
#2: Protein ETHYLBENZENE DEHYDROGENASE BETA-SUBUNIT


Mass: 39737.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: AZOARCUS SP. EBN1 RENAMED TO AROMATOLEUM AROMATICUM
Source: (natural) AROMATOLEUM AROMATICUM (bacteria) / Strain: EBN1 / References: UniProt: Q5P5I1, EC: 1.17.99.2
#3: Protein ETHYLBENZENE DEHYDROGENASE GAMMA-SUBUNIT


Mass: 23093.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: AZOARCUS SP. EBN1 RENAMED TO AROMATOLEUM AROMATICUM
Source: (natural) AROMATOLEUM AROMATICUM (bacteria) / Strain: EBN1 / References: UniProt: Q5P5I2, EC: 1.17.99.2

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Non-polymers , 11 types, 839 molecules

#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo
#9: Chemical ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#10: Chemical ChemComp-MD1 / PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER


Mass: 740.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#11: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#12: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#13: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 818 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.5 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.24
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 127864 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.8
Reflection shellResolution: 1.88→1.94 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.8 / % possible all: 80.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.88→46.42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.993 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.183 6423 5 %RANDOM
Rwork0.148 ---
obs0.15 121438 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å2-0.32 Å2
2---0.88 Å20 Å2
3---1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.88→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11571 0 250 818 12639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02212161
X-RAY DIFFRACTIONr_bond_other_d0.0020.028369
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.97716506
X-RAY DIFFRACTIONr_angle_other_deg0.9983.00120209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68951460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46823.352549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.602151981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6851579
X-RAY DIFFRACTIONr_chiral_restr0.1160.21694
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213457
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022551
X-RAY DIFFRACTIONr_nbd_refined0.2070.22848
X-RAY DIFFRACTIONr_nbd_other0.2120.29825
X-RAY DIFFRACTIONr_nbtor_refined0.1910.26009
X-RAY DIFFRACTIONr_nbtor_other0.0910.26308
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2912
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0311.59171
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.174211652
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17435922
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8674.54797
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: 1.88→1.93 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 381
Rwork0.191 6970
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)
10.7082-0.08110.04760.6739-0.09030.2936-0.0181-0.17580.07210.16110.02340.0657-0.0426-0.0398-0.0053-0.0969-0.00050.0364-0.088-0.0107-0.105128.193134.741717.3356
20.653-0.07170.04870.6414-0.02670.66480.01270.1256-0.0229-0.1423-0.01930.00960.01570.04050.0065-0.09910.0010.0022-0.1184-0.0013-0.132736.366226.1966-16.8082
32.1362-0.34451.22052.0441-0.84653.0278-0.02240.25180.1445-0.38750.07830.2603-0.0432-0.1226-0.05590.1267-0.0425-0.1190.05230.0152-0.050114.442727.1924-52.7719
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A65 - 976
2X-RAY DIFFRACTION1A1984
3X-RAY DIFFRACTION2B16 - 352
4X-RAY DIFFRACTION2B1356
5X-RAY DIFFRACTION2B1359
6X-RAY DIFFRACTION3C1 - 214
7X-RAY DIFFRACTION3C1217

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