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- PDB-2e7z: Acetylene Hydratase from Pelobacter acetylenicus -

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Basic information

Entry
Database: PDB / ID: 2e7z
TitleAcetylene Hydratase from Pelobacter acetylenicus
ComponentsAcetylene hydratase Ahy
KeywordsLYASE / tungstoprotein / DMSO reductase family / iron-sulfur-cluster
Function / homology
Function and homology information


acetylene hydratase / acetylene hydratase activity / molybdopterin cofactor binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Acetylene hydratase, MopB domain / Acetylene hydratase / ADC-like domains / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases ...Acetylene hydratase, MopB domain / Acetylene hydratase / ADC-like domains / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / N-terminal domain of TfIIb / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Single Sheet / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-MGD / IRON/SULFUR CLUSTER / : / Acetylene hydratase
Similarity search - Component
Biological speciesPelobacter acetylenicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.26 Å
AuthorsEinsle, O. / Kroneck, P.M.H. / Seiffert, G.B. / Messerschmidt, A.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase
Authors: Seiffert, G.B. / Ullmann, G.M. / Messerschmidt, A. / Schink, B. / Kroneck, P.M.H. / Einsle, O.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization and preliminary X-ray analysis of the tungsten-dependent acetylene hydratase from Pelobacter acetylenicus
Authors: Einsle, O. / Niessen, H. / Abt, D.J. / Seiffert, G. / Schink, B. / Huber, R. / Messerschmidt, A. / Kroneck, P.M.H.
History
DepositionJan 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Sep 4, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn_source / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylene hydratase Ahy
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,9869
Polymers81,6511
Non-polymers2,3358
Water15,853880
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.776, 71.971, 106.760
Angle α, β, γ (deg.)90.00, 124.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1467-

HOH

21A-1635-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acetylene hydratase Ahy


Mass: 81650.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pelobacter acetylenicus (bacteria) / Strain: WoAcy / References: UniProt: Q71EW5, EC: 4.2.1.71

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Non-polymers , 7 types, 888 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: 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.: 2 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#6: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: W
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 880 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 21% PEG 8000, 0.3M MgAcetate, 0.1M NaCacodylate, 0.04M NaAzide, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONMPG/DESY, HAMBURG BW611.738
SYNCHROTRONEMBL/DESY, HAMBURG X1121.05
Detector
TypeIDDetectorDateDetails
MAR CCD 165 mm1CCDAug 2, 2006mirrors
MAR CCD 165 mm2CCDAug 2, 2006mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1graphiteSINGLE WAVELENGTHMx-ray1
2graphiteSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.7381
21.051
ReflectionResolution: 1.26→50 Å / Num. all: 203457 / Num. obs: 194301 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.85 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 19.6
Reflection shellResolution: 1.26→1.35 Å / Redundancy: 1.65 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 1.91 / Num. unique all: 35051 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345CCDdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.26→30.63 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.02 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19512 9771 5 %RANDOM
Rwork0.15953 ---
obs0.16132 184521 95.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.183 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-0.18 Å2
2--1.2 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.26→30.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7633 0 155 928 8716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228035
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.99210980
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0115991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06124.746354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.631151325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0721536
X-RAY DIFFRACTIONr_chiral_restr0.0890.21177
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026149
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.23155
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.24207
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2849
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3070.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.252
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.390.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0911.54865
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66327868
X-RAY DIFFRACTIONr_scbond_it2.66233334
X-RAY DIFFRACTIONr_scangle_it3.7964.53090
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 688 -
Rwork0.323 13041 -
obs--91.99 %

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