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- PDB-4qup: Crystal structure of stachydrine demethylase with N-methyl prolin... -

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Basic information

Entry
Database: PDB / ID: 4qup
TitleCrystal structure of stachydrine demethylase with N-methyl proline from low X-ray dose composite datasets
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 / : / FE2/S2 (INORGANIC) CLUSTER / COBALT HEXAMMINE(III) / Ring-hydroxylating dioxygenase
Similarity search - Component
Biological speciesSinorhizobium meliloti 1021 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 / pdbx_struct_special_symmetry / 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_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_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

Downloads & links

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Assembly

Deposited unit
A: Monoxygenase; demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8527
Polymers49,1151
Non-polymers7366
Water4,684260
1
A: Monoxygenase; demethylase
hetero molecules

A: Monoxygenase; demethylase
hetero molecules

A: Monoxygenase; demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,55521
Polymers147,3463
Non-polymers2,20918
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 area12270 Å2
ΔGint-81 kcal/mol
Surface area43430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.746, 97.746, 177.984
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-506-

NCO

21A-506-

NCO

31A-506-

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 , 7 types, 266 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-3BY / 1-methyl-L-proline


Type: L-peptide linking / Mass: 129.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO2
#5: 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
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% PEG3350, 10% glycerol, 100 mM HEPES, pH 7.0, 25 mM hexamminecobalt chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 4, 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: 1.7→50 Å / Num. all: 55766 / Num. obs: 55766 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 10 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VCA

3vca


Resolution: 1.7→34.48 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.894 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 2822 5.1 %RANDOM
Rwork0.18188 ---
obs0.18367 52900 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.286 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3265 0 35 260 3560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193388
X-RAY DIFFRACTIONr_bond_other_d0.0040.023130
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.9544621
X-RAY DIFFRACTIONr_angle_other_deg1.0383.0027181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.475412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02123.481158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26715517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0381522
X-RAY DIFFRACTIONr_chiral_restr0.1270.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213841
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02809
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 186 -
Rwork0.229 3783 -
obs--97.59 %

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