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- PDB-5b01: Structure of a prenyltransferase in its unbound form -

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Basic information

Entry
Database: PDB / ID: 5b01
TitleStructure of a prenyltransferase in its unbound form
ComponentsMoeN5
KeywordsTRANSFERASE / prenyltransferase / alpha-helical fold
Function / homologyFarnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha / MoeN5
Function and homology information
Biological speciesStreptomyces ghanaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsKo, T.-P. / Zhang, L. / Chen, C.-C. / Guo, R.-T.
CitationJournal: To Be Published
Title: Structure and function of a prenyltransferase
Authors: Zhang, L. / Chen, C.-C. / Ko, T.-P. / Guo, R.-T. / Oldfield, E.O.
History
DepositionOct 27, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _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: MoeN5
B: MoeN5
C: MoeN5
D: MoeN5
E: MoeN5
F: MoeN5
G: MoeN5
H: MoeN5
I: MoeN5
J: MoeN5


Theoretical massNumber of molelcules
Total (without water)322,58310
Polymers322,58310
Non-polymers00
Water0
1
A: MoeN5
B: MoeN5


Theoretical massNumber of molelcules
Total (without water)64,5172
Polymers64,5172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-34 kcal/mol
Surface area19850 Å2
MethodPISA
2
C: MoeN5
D: MoeN5


Theoretical massNumber of molelcules
Total (without water)64,5172
Polymers64,5172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-36 kcal/mol
Surface area19960 Å2
MethodPISA
3
E: MoeN5
F: MoeN5


Theoretical massNumber of molelcules
Total (without water)64,5172
Polymers64,5172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-36 kcal/mol
Surface area19940 Å2
MethodPISA
4
G: MoeN5
H: MoeN5


Theoretical massNumber of molelcules
Total (without water)64,5172
Polymers64,5172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-33 kcal/mol
Surface area19990 Å2
MethodPISA
5
I: MoeN5
J: MoeN5


Theoretical massNumber of molelcules
Total (without water)64,5172
Polymers64,5172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-33 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.604, 106.604, 310.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
MoeN5 / prenyltransferase


Mass: 32258.320 Da / Num. of mol.: 10
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.1 / Details: 0.2M 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: 3.45→25 Å / Num. obs: 44521 / % possible obs: 98.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 12.7
Reflection shellResolution: 3.45→3.57 Å / Redundancy: 4 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B00

5b00


Resolution: 3.45→25 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2090 5 %Random
Rwork0.225 ---
obs-41758 92.3 %-
Refine analyzeLuzzati coordinate error obs: 0.44 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.6 Å
Refinement stepCycle: LAST / Resolution: 3.45→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20030 0 0 0 20030

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