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- PDB-4qur: Crystal Structure of stachydrine demethylase in complex with cyan... -

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Basic information

Entry
Database: PDB / ID: 4qur
TitleCrystal Structure of stachydrine demethylase in complex with cyanide, oxygen, and N-methyl proline in a new orientation
Componentsmonoxygenase; demethylaseOxygenase
KeywordsOXIDOREDUCTASE / composite datasets / photoelectron / enzyme-catalyzed reactions / cyanide / synchrotron / Rieske type monoxygenase
Function / homology
Function and homology information


dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich ...Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1-methyl-L-proline / CYANIDE ION / : / FE2/S2 (INORGANIC) CLUSTER / COBALT HEXAMMINE(III) / OXYGEN MOLECULE / Ring-hydroxylating dioxygenase
Similarity search - Component
Biological speciesSinorhizobium meliloti 1021 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.759 Å
AuthorsAgarwal, R. / Andi, B. / Gizzi, A. / Bonanno, J.B. / Almo, S.C. / Orville, A.M.
CitationJournal: To be Published
Title: Tracking photoelectron induced in-crystallo enzyme catalysis
Authors: Agarwal, R. / Andi, B. / Gizzi, A. / Bonanno, J.B. / Almo, S.C. / Orville, A.M.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Non-polymer description
Revision 1.2Mar 9, 2016Group: Structure summary
Revision 1.3Sep 20, 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_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr2_label_alt_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_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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: monoxygenase; demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8178
Polymers49,1151
Non-polymers7027
Water4,594255
1
A: monoxygenase; demethylase
hetero molecules

A: monoxygenase; demethylase
hetero molecules

A: monoxygenase; demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,45224
Polymers147,3463
Non-polymers2,10621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_785-y+2,x-y+3,z1
crystal symmetry operation3_475-x+y-1,-x+2,z1
Buried area12770 Å2
ΔGint-131 kcal/mol
Surface area43230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.065, 98.065, 178.654
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-504-

NCO

21A-504-

NCO

31A-504-

NCO

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Components

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Protein , 1 types, 1 molecules A

#1: Protein monoxygenase; demethylase / Oxygenase / Stachydrine demethylase


Mass: 49115.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti 1021 (bacteria) / Gene: SMa0751 / Plasmid: pSGC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92ZP9, Oxidoreductases

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Non-polymers , 8 types, 262 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#6: Chemical ChemComp-3BY / 1-methyl-L-proline


Type: L-peptide linking / Mass: 129.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO2
#7: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#8: Chemical ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 5% PEG3350, 10% glycerol, 100 mM HEPES, 25 mM hexamminecobalt chloride, 100 mM stachydrine, pH 7.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2013 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.759→50 Å / Num. all: 51099 / Num. obs: 51099 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 42.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.4
Reflection shellResolution: 1.759→1.83 Å / Redundancy: 36.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
PHENIX(phenix.refine: dev_1423)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VCA

3vca


Resolution: 1.759→34.574 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 2580 5.07 %
Rwork0.2033 --
obs0.2046 50842 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.759→34.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3273 0 33 255 3561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123394
X-RAY DIFFRACTIONf_angle_d1.3414628
X-RAY DIFFRACTIONf_dihedral_angle_d13.9781224
X-RAY DIFFRACTIONf_chiral_restr0.083497
X-RAY DIFFRACTIONf_plane_restr0.007598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.759-1.79330.23811440.23162613X-RAY DIFFRACTION100
1.7933-1.82990.2891250.22882657X-RAY DIFFRACTION100
1.8299-1.86970.23891220.23252672X-RAY DIFFRACTION100
1.8697-1.91320.30361450.25262594X-RAY DIFFRACTION99
1.9132-1.9610.29491300.24232653X-RAY DIFFRACTION99
1.961-2.0140.20971640.21632607X-RAY DIFFRACTION100
2.014-2.07330.27241580.21542654X-RAY DIFFRACTION100
2.0733-2.14020.26691560.22172634X-RAY DIFFRACTION100
2.1402-2.21670.29251310.22042660X-RAY DIFFRACTION100
2.2167-2.30540.26751290.23832560X-RAY DIFFRACTION96
2.3054-2.41030.27611300.21662676X-RAY DIFFRACTION100
2.4103-2.53740.23031430.21742696X-RAY DIFFRACTION100
2.5374-2.69630.26421690.2152659X-RAY DIFFRACTION100
2.6963-2.90440.23891270.21152724X-RAY DIFFRACTION100
2.9044-3.19640.23291490.21262717X-RAY DIFFRACTION100
3.1964-3.65850.22431420.1912735X-RAY DIFFRACTION100
3.6585-4.60760.16721630.16832768X-RAY DIFFRACTION100
4.6076-34.58070.2011530.1862983X-RAY DIFFRACTION100

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