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- PDB-5cob: Crystal structure of iridoid synthase in complex with NADP+ and 8... -

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Basic information

Entry
Database: PDB / ID: 5cob
TitleCrystal structure of iridoid synthase in complex with NADP+ and 8-oxogeranial at 2.65-angstrom resolution
ComponentsIridoid synthase
KeywordsOXIDOREDUCTASE / SDR / P5bR / Rossmann fold / 1-4 addition
Function / homology
Function and homology information


(S)-8-oxocitronellyl enol synthase / monoterpenoid biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / (2E,6E)-2,6-dimethylocta-2,6-dienedial / (S)-8-oxocitronellyl enol synthase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.65 Å
AuthorsQin, L. / Zhu, Y. / Ding, Z. / Zhang, X. / Ye, S. / Zhang, R.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Structure of iridoid synthase in complex with NADP(+)/8-oxogeranial reveals the structural basis of its substrate specificity.
Authors: Qin, L. / Zhu, Y. / Ding, Z. / Zhang, X. / Ye, S. / Zhang, R.
History
DepositionJul 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iridoid synthase
B: Iridoid synthase
C: Iridoid synthase
D: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,27316
Polymers164,8574
Non-polymers4,41512
Water3,369187
1
A: Iridoid synthase
B: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6368
Polymers82,4292
Non-polymers2,2086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Iridoid synthase
D: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6368
Polymers82,4292
Non-polymers2,2086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.988, 171.914, 66.032
Angle α, β, γ (deg.)90.00, 89.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Iridoid synthase


Mass: 41214.305 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 26-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Production host: Escherichia coli (E. coli) / References: UniProt: K7WDL7, EC: 1.3.1.99
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-XOG / (2E,6E)-2,6-dimethylocta-2,6-dienedial / 8-oxogeranial / 8-Oxogeranial


Mass: 166.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14O2
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.98 M ammonium sulfate, 1% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.65→36.137 Å / Num. obs: 43695 / % possible obs: 98.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.6
Reflection shellResolution: 2.65→2.71 Å / Redundancy: 5 % / Rmerge(I) obs: 0.266 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.65→36.137 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 2112 5.03 %
Rwork0.1944 --
obs0.1971 42018 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→36.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11580 0 292 187 12059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312180
X-RAY DIFFRACTIONf_angle_d0.82716536
X-RAY DIFFRACTIONf_dihedral_angle_d14.4284472
X-RAY DIFFRACTIONf_chiral_restr0.0521804
X-RAY DIFFRACTIONf_plane_restr0.0042064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.71160.35871530.252609X-RAY DIFFRACTION99
2.7116-2.77940.36171280.2532677X-RAY DIFFRACTION99
2.7794-2.85450.30491520.24072669X-RAY DIFFRACTION99
2.8545-2.93850.32731320.25442638X-RAY DIFFRACTION99
2.9385-3.03330.30731420.24312656X-RAY DIFFRACTION98
3.0333-3.14160.26631200.23272672X-RAY DIFFRACTION97
3.1416-3.26740.30831240.22112564X-RAY DIFFRACTION96
3.2674-3.4160.28531380.20562669X-RAY DIFFRACTION100
3.416-3.59590.23761680.19012691X-RAY DIFFRACTION100
3.5959-3.8210.22231170.18822672X-RAY DIFFRACTION99
3.821-4.11560.20331360.17122736X-RAY DIFFRACTION99
4.1156-4.52910.21921460.1672627X-RAY DIFFRACTION99
4.5291-5.18280.19851540.16112645X-RAY DIFFRACTION98
5.1828-6.52350.21851470.19052704X-RAY DIFFRACTION100
6.5235-36.14070.22721550.17692677X-RAY DIFFRACTION98
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)
13.2818-0.4379-0.02631.20980.48930.6965-0.1908-0.3282-0.59220.28330.1011-0.06370.114-0.05630.07610.39080.0046-0.00070.3380.16090.4261-6.6346-19.028724.1115
26.1182-4.0281-2.90276.7183-2.84478.3532-0.0610.7878-0.4351-0.51010.22121.47441.1407-1.1001-0.1630.6307-0.1205-0.09960.3986-0.00210.6756-20.1028-1.05436.7349
31.1978-0.0477-0.47941.67870.07842.4163-0.17440.093-0.3524-0.19530.05190.00920.3066-0.10380.12090.342-0.04280.03340.2950.0420.4878-5.5313-16.20833.0711
42.7775-1.75620.54672.8431-1.54863.7853-0.3646-0.52260.22820.38260.1268-0.5851-0.77720.08030.33390.7219-0.1329-0.03840.3545-0.01450.296723.560119.03650.8578
50.8727-0.14920.62561.93950.13192.85290.03430.14210.1392-0.1240.1025-0.2598-0.45610.3206-0.11240.4639-0.11520.00780.37910.00990.305524.158518.6964-8.3828
67.39882.2329-2.53966.61913.76594.3279-0.08951.27520.6407-1.63670.24890.3516-0.1961-1.0594-0.01850.79310.0178-0.09620.58270.09820.50536.47580.7703-20.1198
72.2965-0.1654-0.40331.6318-0.05221.66920.08130.09410.3189-0.03940.11470.179-0.4369-0.0997-0.18740.5385-0.04520.03540.2890.05390.32753.033515.9332-5.556
84.355-2.53261.50664.19991.3633.38750.1624-0.6103-0.5650.30810.25360.31330.1953-0.0789-0.32360.7822-0.1379-0.00260.31070.0740.2779.781923.673133.9164
92.1544-0.1274-0.69552.8649-0.78911.18270.07390.1501-0.1793-0.0659-0.04390.18790.3831-0.2079-0.03920.6216-0.1414-0.01660.3519-0.02690.24069.157223.996324.694
108.78061.75434.84944.1022-1.24454.32160.15021.112-0.7359-1.08760.3687-0.51260.55610.7464-0.39640.9146-0.00220.080.3736-0.07780.70226.567141.881412.8264
112.4474-0.21630.64521.340.01461.25360.02340.1458-0.378-0.02030.0905-0.20070.29440.0671-0.11030.6479-0.0454-0.0020.3027-0.03250.346430.325326.769327.2917
125.58631.2719-1.14424.4475-2.16784.7139-0.19770.11350.08030.41360.27260.5063-0.2861-0.6607-0.11230.28520.02320.0260.3466-0.13160.667529.915361.025356.2161
131.72030.0287-0.16742.3807-0.11651.2788-0.0289-0.35480.34030.03320.0656-0.2029-0.22250.1648-0.00140.29330.0133-0.03170.3787-0.1470.428743.251761.995957.111
146.0506-2.17735.7185.59532.18939.1504-0.56340.98670.6569-0.61370.4133-1.7322-0.97311.37810.0310.7034-0.1230.12230.4202-0.01830.787253.474443.787839.7224
151.5474-0.29040.70931.6929-0.62642.8978-0.12180.0650.249-0.28850.0625-0.0516-0.41530.09970.0660.3724-0.04890.00090.3-0.0560.483138.90958.909335.8371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 148 )
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 176 )
3X-RAY DIFFRACTION3chain 'A' and (resid 177 through 388 )
4X-RAY DIFFRACTION4chain 'B' and (resid 24 through 48 )
5X-RAY DIFFRACTION5chain 'B' and (resid 49 through 148 )
6X-RAY DIFFRACTION6chain 'B' and (resid 149 through 176 )
7X-RAY DIFFRACTION7chain 'B' and (resid 177 through 388 )
8X-RAY DIFFRACTION8chain 'C' and (resid 24 through 48 )
9X-RAY DIFFRACTION9chain 'C' and (resid 49 through 148 )
10X-RAY DIFFRACTION10chain 'C' and (resid 149 through 176 )
11X-RAY DIFFRACTION11chain 'C' and (resid 177 through 388 )
12X-RAY DIFFRACTION12chain 'D' and (resid 24 through 58 )
13X-RAY DIFFRACTION13chain 'D' and (resid 59 through 148 )
14X-RAY DIFFRACTION14chain 'D' and (resid 149 through 176 )
15X-RAY DIFFRACTION15chain 'D' and (resid 177 through 388 )

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