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- PDB-2fp8: Structure of Strictosidine Synthase, the Biosynthetic Entry to th... -

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Basic information

Entry
Database: PDB / ID: 2fp8
TitleStructure of Strictosidine Synthase, the Biosynthetic Entry to the Monoterpenoid Indole Alkaloid Family
ComponentsStrictosidine synthase
KeywordsLYASE / six bladed beta propeller fold / STR1 / Synthase
Function / homology
Function and homology information


strictosidine synthase / strictosidine synthase activity / alkaloid metabolic process / vacuole / biosynthetic process
Similarity search - Function
Strictosidine synthase, conserved region / Strictosidine synthase / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Strictosidine synthase
Similarity search - Component
Biological speciesRauvolfia serpentina (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsPanjikar, S.
CitationJournal: Plant Cell / Year: 2006
Title: The structure of Rauvolfia serpentina strictosidine synthase is a novel six-bladed beta-propeller fold in plant proteins
Authors: Ma, X. / Panjikar, S. / Koepke, J. / Loris, E. / Stockigt, J.
History
DepositionJan 16, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Strictosidine synthase
B: Strictosidine synthase


Theoretical massNumber of molelcules
Total (without water)71,5322
Polymers71,5322
Non-polymers00
Water7,224401
1
A: Strictosidine synthase


Theoretical massNumber of molelcules
Total (without water)35,7661
Polymers35,7661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Strictosidine synthase


Theoretical massNumber of molelcules
Total (without water)35,7661
Polymers35,7661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.290, 147.290, 122.331
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLU / End label comp-ID: VAL / Refine code: 2 / Auth seq-ID: 33 - 332 / Label seq-ID: 11 - 310

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Strictosidine synthase /


Mass: 35765.938 Da / Num. of mol.: 2
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): M15[pREP4] / References: UniProt: P68175, strictosidine synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 3.62 Å3/Da / Density % sol: 65.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: 0.8M potassium sodium tartrate tetrahydrate, 100mM HEPES-Na, 1mM Tryptamine, pH 7.5, VAPOR DIFFUSION, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.9714, 0.9813, 0.9822
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 13, 2004
RadiationMonochromator: SILICON 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97141
20.98131
30.98221
ReflectionResolution: 2.3→20 Å / Num. all: 45048 / Num. obs: 42594 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 3.2
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.37 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.252 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.215 / ESU R Free: 0.177 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21743 1121 2.6 %RANDOM
Rwork0.18771 ---
all0.192 45048 --
obs0.18848 42594 99.72 %-
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: 24.775 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å21.72 Å20 Å2
2--3.45 Å20 Å2
3----5.17 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4772 0 0 401 5173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214906
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9456675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7725603
X-RAY DIFFRACTIONr_chiral_restr0.1130.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023808
X-RAY DIFFRACTIONr_nbd_refined0.2250.22189
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2367
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.213
X-RAY DIFFRACTIONr_mcbond_it0.6421.53003
X-RAY DIFFRACTIONr_mcangle_it1.2472.54860
X-RAY DIFFRACTIONr_scbond_it2.98451903
X-RAY DIFFRACTIONr_scangle_it4.399101815
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
1200tight positional0.080.05
1161medium positional0.370.5
1200tight thermal0.581.5
1161medium thermal1.382.5
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.262 88
Rwork0.237 3041
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)
11.5513-0.58360.35161.04870.04293.9936-0.05730.0421-0.09310.06820.11890.04040.0151-0.1886-0.06160.00530.01720.01120.06410.00070.180795.544175.6880.0239
23.0337-1.14121.11161.6531-0.1055.18190.28570.3379-0.1173-0.3844-0.2867-0.11220.59440.97370.00090.30210.33810.02850.4608-0.00410.2931129.180551.0406-15.8608
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA32 - 33310 - 311
2X-RAY DIFFRACTION2BB32 - 33310 - 311

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