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- PDB-5b00: Structure of the prenyltransferase MoeN5 in complex with geranyl ... -

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Basic information

Entry
Database: PDB / ID: 5b00
TitleStructure of the prenyltransferase MoeN5 in complex with geranyl pyrophosphate
ComponentsMoeN5
KeywordsTRANSFERASE / prenyltransferase / alpha-helical fold
Function / homologyFarnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha / GERANYL DIPHOSPHATE / MoeN5
Function and homology information
Biological speciesStreptomyces ghanaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsKo, T.-P. / Zhang, L. / Chen, C.-C. / Guo, R.-T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Moenomycin Biosynthesis: Structure and Mechanism of Action of the Prenyltransferase MoeN5.
Authors: Zhang, L. / Chen, C.C. / Ko, T.P. / Huang, J.W. / Zheng, Y. / Liu, W. / Wang, I. / Malwal, S.R. / Feng, X. / Wang, K. / Huang, C.H. / Hsu, S.T. / Wang, A.H. / Oldfield, E. / Guo, R.T.
History
DepositionOct 27, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 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

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Assembly

Deposited unit
A: MoeN5
B: MoeN5
C: MoeN5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7186
Polymers96,7753
Non-polymers9433
Water3,441191
1
A: MoeN5
hetero molecules

A: MoeN5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1454
Polymers64,5172
Non-polymers6282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5240 Å2
ΔGint-31 kcal/mol
Surface area20060 Å2
MethodPISA
2
B: MoeN5
C: MoeN5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1454
Polymers64,5172
Non-polymers6282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-27 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.850, 58.547, 92.678
Angle α, β, γ (deg.)90.00, 91.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MoeN5 / prenyltransferase


Mass: 32258.320 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces ghanaensis (bacteria) / Gene: moeN5 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A010
#2: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE / Geranyl pyrophosphate


Mass: 314.209 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H20O7P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.57 % / Description: hicup uppsala
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.1 / Details: 0.2 M Na2HPO4, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→25 Å / Num. obs: 23648 / % possible obs: 99 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 19.9
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 3.5 / % possible all: 93.4

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.95→25 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.337 1053 5 %Random
Rwork0.287 ---
obs-21519 90.8 %-
Refine analyzeLuzzati coordinate error obs: 0.67 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 1.16 Å
Refinement stepCycle: LAST / Resolution: 2.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5985 0 57 191 6233

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