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- PDB-2wfl: Crystal structure of polyneuridine aldehyde esterase -

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Basic information

Entry
Database: PDB / ID: 2wfl
TitleCrystal structure of polyneuridine aldehyde esterase
Components(POLYNEURIDINE-ALDEHYDE ESTERASE) x 2
KeywordsHYDROLASE / ALKALOID METABOLISM / MONOTERPENOID INDOLE ALKALOIDS / PNAE / SERINE ESTERASE
Function / homology
Function and homology information


polyneuridine-aldehyde esterase / polyneuridine-aldehyde esterase activity / indole alkaloid metabolic process / jasmonic acid metabolic process / methyl salicylate esterase activity / methyl indole-3-acetate esterase activity / methyl jasmonate esterase activity / salicylic acid metabolic process
Similarity search - Function
Methylesterase/Alpha-hydroxynitrile lyase / Alpha/beta hydrolase family / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyneuridine aldehyde esterase
Similarity search - Component
Biological speciesRAUVOLFIA SERPENTINA (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYang, L. / Hill, M. / Panjikar, S. / Wang, M. / Stoeckigt, J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: Structural Basis and Enzymatic Mechanism of the Biosynthesis of C9- from C10-Monoterpenoid Indole Alkaloids.
Authors: Yang, L. / Hill, M. / Wang, M. / Panjikar, S. / Stockigt, J.
History
DepositionApr 8, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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: POLYNEURIDINE-ALDEHYDE ESTERASE
B: POLYNEURIDINE-ALDEHYDE ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8034
Polymers59,6112
Non-polymers1922
Water5,459303
1
A: POLYNEURIDINE-ALDEHYDE ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8642
Polymers29,7671
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: POLYNEURIDINE-ALDEHYDE ESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9402
Polymers29,8441
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.758, 176.917, 75.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNARGARGAA9 - 549 - 54
21GLNGLNARGARGBB9 - 549 - 54
12THRTHRMETMETAA60 - 11360 - 113
22THRTHRMETMETBB60 - 11360 - 113
13LEULEUSERSERAA157 - 262157 - 262
23LEULEUSERSERBB157 - 262157 - 262

NCS oper: (Code: given
Matrix: (0.7085, 0.6818, 0.182), (0.6858, -0.726, 0.05036), (0.1665, 0.08917, -0.982)
Vector: -73.44, 173.2, 43.62)

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Components

#1: Protein POLYNEURIDINE-ALDEHYDE ESTERASE


Mass: 29767.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RAUVOLFIA SERPENTINA (serpentwood) / Plasmid: PQE-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15PREP4
References: UniProt: Q9SE93, polyneuridine-aldehyde esterase
#2: Protein POLYNEURIDINE-ALDEHYDE ESTERASE


Mass: 29843.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RAUVOLFIA SERPENTINA (serpentwood) / Plasmid: PQE-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15PREP4
References: UniProt: Q9SE93, polyneuridine-aldehyde esterase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.64 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 6.8
Details: 0.20M BIS-TRIS, 0.25M LI2SO4, 25%POLYETHYLENE GLYCOL 3350, PH6.30., pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8
DetectorType: MARRESEARCH / Detector: CCD / Details: DOUBLE CRYSTAL SI 111
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 36861 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 38.42 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 32.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
Auto-Rickshawphasing
MOLREPphasing
REFMAC5.4.0069refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XKL

1xkl


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.78 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1046 2.8 %RANDOM
Rwork0.182 ---
obs0.183 35684 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.17 Å2
Baniso -1Baniso -2Baniso -3
1-3.17 Å20 Å20 Å2
2---1.32 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 10 303 4347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224146
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.9795566
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.555502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09924.659176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.99515741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1041514
X-RAY DIFFRACTIONr_chiral_restr0.1220.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213072
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_it0.8991.52548
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6262.54086
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6351598
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.229101480
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A820tight positional0.060.05
2B820tight positional0.060.05
1A797medium positional0.220.5
2B797medium positional0.220.5
1A820tight thermal0.220.5
2B820tight thermal0.220.5
1A797medium thermal0.32
2B797medium thermal0.32
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 77 -
Rwork0.197 2599 -
obs--100 %
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)
13.26270.6366-0.23492.6489-0.60942.74340.08460.1758-0.3988-0.3401-0.1053-0.11320.38450.00490.0207-0.10910.0724-0.0301-0.1664-0.0517-0.148926.3615104.613318.9323
23.72231.05440.17823.731.81933.82140.10310.3797-0.2945-0.4545-0.053-0.30660.49970.3896-0.05020.02620.15280.0274-0.042-0.0573-0.158533.0912106.5379.0303
32.7187-0.4033-0.1872.05220.09062.50490.20030.4894-0.061-0.5389-0.06890.12350.142-0.1995-0.1314-0.04270.0881-0.055-0.087-0.0272-0.138620.4344113.955910.5591
46.501-1.28031.0912.89420.03142.4192-0.0669-0.02060.24930.11030.01290.2217-0.1706-0.23480.054-0.20790.03290.006-0.2150.0022-0.187519.7378115.625238.9784
54.52150.0487-0.43623.02411.25522.8976-0.039-0.29870.19720.32010.08980.0239-0.1515-0.0205-0.0508-0.11090.05740.0136-0.1389-0.0121-0.186623.9437117.930450.1232
61.6015-0.18840.03052.48480.53842.07070.0042-0.3765-0.17490.41480.0590.3250.2978-0.2524-0.0633-0.11220.01030.0351-0.10090.05-0.076420.327104.028946.6786
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 54
2X-RAY DIFFRACTION2A60 - 113
3X-RAY DIFFRACTION3A157 - 262
4X-RAY DIFFRACTION4B9 - 54
5X-RAY DIFFRACTION5B60 - 113
6X-RAY DIFFRACTION6B157 - 262

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