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- PDB-5bp8: ent-Copalyl diphosphate synthase from Streptomyces platensis -

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Basic information

Entry
Database: PDB / ID: 5bp8
Titleent-Copalyl diphosphate synthase from Streptomyces platensis
ComponentsEnt-copalyl diphosphate synthase
KeywordsISOMERASE / ent-copalyl diphosphate synthase / PtmT2 / structural genomics / APC109899 / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro / PSI-Biology
Function / homology
Function and homology information


diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding
Similarity search - Function
: / Squalene cyclase, C-terminal / Squalene-hopene cyclase C-terminal domain / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid
Similarity search - Domain/homology
Ent-copalyl diphosphate synthase
Similarity search - Component
Biological speciesStreptomyces platensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsOsipiuk, J. / Hatzos-Skintges, C. / Endres, M. / Babnigg, G. / Rudolf, J.D. / Ma, M. / Chang, C.-Y. / Shen, B. / Joachimiak, A. / Enzyme Discovery for Natural Product Biosynthesis (NatPro) / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Structure of the ent-Copalyl Diphosphate Synthase PtmT2 from Streptomyces platensis CB00739, a Bacterial Type II Diterpene Synthase.
Authors: Rudolf, J.D. / Dong, L.B. / Cao, H. / Hatzos-Skintges, C. / Osipiuk, J. / Endres, M. / Chang, C.Y. / Ma, M. / Babnigg, G. / Joachimiak, A. / Phillips, G.N. / Shen, B.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ent-copalyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4367
Polymers54,8931
Non-polymers5426
Water9,548530
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ent-copalyl diphosphate synthase
hetero molecules

A: Ent-copalyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,87114
Polymers109,7862
Non-polymers1,08512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area3930 Å2
ΔGint-150 kcal/mol
Surface area38200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.870, 132.870, 190.748
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1274-

HOH

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Components

#1: Protein Ent-copalyl diphosphate synthase


Mass: 54893.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces platensis (bacteria) / Gene: ptmT2 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A023VSF1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.5 M ammonium sulfate, 0.1 M Bis-Tris propane buffer, 5 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2015
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 59533 / Num. obs: 59533 / % possible obs: 99.4 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.026 / Rrim(I) all: 0.082 / Χ2: 1.361 / Net I/av σ(I): 32.596 / Net I/σ(I): 9.5 / Num. measured all: 545528
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.835.40.635227490.7810.290.7020.70893.3
1.83-1.865.90.55628670.8250.2420.610.72296.8
1.86-1.96.60.47529590.8850.1940.5150.74999.4
1.9-1.947.90.41829310.930.1570.4470.775100
1.94-1.988.70.34230230.9620.1220.3630.799100
1.98-2.039.70.28629830.9760.0960.3020.837100
2.03-2.08100.23829470.9840.0790.2510.893100
2.08-2.13100.19429580.9890.0640.2040.945100
2.13-2.2100.16929920.9910.0560.1780.975100
2.2-2.27100.14429770.9930.0480.1521.054100
2.27-2.35100.12429790.9950.0410.1311.117100
2.35-2.44100.11129920.9950.0370.1171.182100
2.44-2.55100.09930230.9960.0330.1041.249100
2.55-2.69100.08429630.9970.0280.0891.372100
2.69-2.86100.07729980.9970.0250.0811.518100
2.86-3.08100.06429880.9980.0210.0681.633100
3.08-3.399.90.0630250.9980.020.0631.829100
3.39-3.889.80.05930100.9980.020.0621.79599.9
3.88-4.889.60.05430440.9980.0180.0572.02499.8
4.88-509.40.05331250.9980.0180.0563.96699

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→42.5 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.131 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 2990 5 %RANDOM
Rwork0.1564 ---
obs0.1579 56537 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.19 Å2 / Biso mean: 27.101 Å2 / Biso min: 13.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0.29 Å20 Å2
2---0.59 Å20 Å2
3---1.91 Å2
Refinement stepCycle: final / Resolution: 1.8→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 29 530 4358
Biso mean--41.18 36.89 -
Num. residues----515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193969
X-RAY DIFFRACTIONr_bond_other_d0.0020.023655
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9725454
X-RAY DIFFRACTIONr_angle_other_deg0.82238409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.425528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.722.822163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79315522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1271534
X-RAY DIFFRACTIONr_chiral_restr0.0790.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214595
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02883
X-RAY DIFFRACTIONr_mcbond_it1.3242.0012073
X-RAY DIFFRACTIONr_mcbond_other1.32222072
X-RAY DIFFRACTIONr_mcangle_it2.0532.9922593
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 219 -
Rwork0.239 3859 -
all-4078 -
obs--93.04 %
Refinement TLS params.Method: refined / Origin x: -2.4477 Å / Origin y: -27.6468 Å / Origin z: -34.1819 Å
111213212223313233
T0.0526 Å20.0009 Å20.0112 Å2-0.0425 Å20.0022 Å2--0.005 Å2
L0.1043 °20.1532 °2-0.1285 °2-0.6644 °2-0.0733 °2--0.2327 °2
S-0.033 Å °-0.0342 Å °-0.0167 Å °-0.1128 Å °0.009 Å °-0.0179 Å °0.0091 Å °0.0285 Å °0.024 Å °

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