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- PDB-2bgh: Crystal structure of Vinorine Synthase -

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Basic information

Entry
Database: PDB / ID: 2bgh
TitleCrystal structure of Vinorine Synthase
ComponentsVINORINE SYNTHASE
KeywordsTRANSFERASE / VS / BAHD / ACETYLTRANSFERASE / AUTO-RICKSHAW
Function / homology
Function and homology information


vinorine synthase / vinorine synthase activity / alkaloid metabolic process
Similarity search - Function
Transferase family / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRAUVOLFIA SERPENTINA (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsMa, X. / Koepke, J. / Panjikar, S. / Fritzsch, G. / Stoeckigt, J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of Vinorine Synthase, the First Representative of the Bahd Superfamily.
Authors: Ma, X. / Koepke, J. / Panjikar, S. / Fritzsch, G. / Stockigt, J.
History
DepositionDec 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 15, 2015Group: Data collection / Database references / Source and taxonomy
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VINORINE SYNTHASE
B: VINORINE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)93,7492
Polymers93,7492
Non-polymers00
Water2,576143
1
A: VINORINE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)46,8741
Polymers46,8741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: VINORINE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)46,8741
Polymers46,8741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.715, 90.455, 136.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A4 - 20
2112B4 - 20
1212A23 - 49
2212B23 - 49
1312A60 - 108
2312B60 - 108
1412A111 - 182
2412B111 - 182
1512A203 - 221
2512B203 - 221
1612A240 - 260
2612B240 - 260
1712A286 - 298
2712B286 - 298
1812A358 - 386
2812B358 - 386
1912A393 - 416
2912B393 - 416

NCS oper: (Code: given
Matrix: (-0.993319, 0.0108, -0.114897), (0.007566, 0.999564, 0.028548), (0.115155, 0.027488, -0.992967)
Vector: 47.25253, -0.57848, 64.56186)

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Components

#1: Protein VINORINE SYNTHASE


Mass: 46874.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RAUVOLFIA SERPENTINA (serpentwood) / Plasmid: PQE2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: Q70PR7, vinorine synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.8 Å3/Da / Density % sol: 0.56 %
Crystal growpH: 6
Details: 0.1 M TRIS-HCL PH 8.7, 2M AMMONIUM SULPHATE, 2% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9714
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9714 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 31740 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 7.1
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 29 / % possible all: 99.1

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Processing

Software
NameVersionClassification
DMmodel building
SCALEPACKdata scaling
Auto-Rickshawphasing
SHELXDphasing
MLPHAREphasing
DMphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.91 / SU B: 26.165 / SU ML: 0.274 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.695 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1004 3.2 %RANDOM
Rwork0.211 ---
obs0.213 30713 98.6 %-
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: 64.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å20 Å2
2--2.15 Å20 Å2
3----4.05 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6465 0 0 143 6608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226631
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.9729031
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6175821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64624.897290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.222151110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7921528
X-RAY DIFFRACTIONr_chiral_restr0.1360.21029
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025016
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.22992
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.24430
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2243
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6251.54257
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.172.56724
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.16852682
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.77102307
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

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1080tight positional0.050.05
1030medium positional0.370.5
1080tight thermal0.471.5
1030medium thermal1.22.5
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 63
Rwork0.306 2197
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)
12.77950.7907-0.12383.84520.01365.7658-0.0122-0.1299-0.02860.2882-0.026-0.1904-0.241-0.00790.0382-0.47160.0778-0.0357-0.34560.0453-0.215518.8223.4619.15
23.18640.5875-1.63551.0321-0.84015.0957-0.35690.8736-0.219-0.4690.2538-0.02750.1015-0.50030.1032-0.3464-0.02060.0112-0.03140.0405-0.090617.6322.06-4.06
30.8754-0.83840.15173.6241-1.86179.57560.06450.3926-0.0811-0.9861-0.16150.23330.1369-0.66330.097-0.0229-0.0079-0.1278-0.0079-0.0529-0.050718.8223.4619.15
43.2816-0.6999-0.57741.8051-1.25288.559-0.6819-0.668-0.27381.41230.31530.1083-0.97710.06890.36660.73430.3548-0.0637-0.086-0.054-0.021521.0420.6370.63
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 216
2X-RAY DIFFRACTION2A218 - 421
3X-RAY DIFFRACTION3B4 - 216
4X-RAY DIFFRACTION4B218 - 421

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