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- PDB-3vkc: Crystal structure of MoeO5 soaked with pyrophosphate -

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Basic information

Entry
Database: PDB / ID: 3vkc
TitleCrystal structure of MoeO5 soaked with pyrophosphate
ComponentsMoeO5
KeywordsTRANSFERASE / TIM barrel
Function / homology
Function and homology information


phospholipid biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / metal ion binding
Similarity search - Function
FMN-linked oxidoreductases / Geranylgeranylglyceryl phosphate synthase/Heptaprenylglyceryl phosphate synthase / GGGP/HepGP synthase superfamily / PcrB family / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-FPQ / PYROPHOSPHATE 2- / MoeO5
Similarity search - Component
Biological speciesStreptomyces ghanaensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsRen, F. / Ko, T.-P. / Huang, C.-H. / Guo, R.-T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Insights into the mechanism of the antibiotic-synthesizing enzyme MoeO5 from crystal structures of different complexes
Authors: Ren, F. / Ko, T.-P. / Feng, X. / Huang, C.-H. / Chan, H.-C. / Hu, Y. / Wang, K. / Ma, Y. / Liang, P.-H. / Wang, A.H.-J. / Oldfield, E. / Guo, R.-T.
History
DepositionNov 12, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MoeO5
B: MoeO5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1746
Polymers62,1932
Non-polymers9814
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-29 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.735, 59.721, 59.062
Angle α, β, γ (deg.)66.70, 71.15, 65.96
Int Tables number1
Space group name H-MP1

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Components

#1: Protein MoeO5 / 2-cis / trans-farnesyl-3-phosphoglycerate synthase


Mass: 31096.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces ghanaensis (bacteria) / Strain: ATCC 14672 / Gene: moeO5 / Plasmid: pET32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A011
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FPQ / (2R)-3-(phosphonooxy)-2-{[(2Z,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]oxy}propanoic acid


Mass: 390.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H31O7P
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 22% PEG 3350, 0.2M Na-malonate, 10mM MgCl2, 100mM Na-pyrophosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Aug 10, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→25 Å / Num. all: 61957 / Num. obs: 59540 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 37.1
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 4 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 9.4 / Num. unique all: 5880 / % possible all: 94.8

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Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3VK5

3vk5


Resolution: 1.66→25 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1856 2988 -random
Rwork0.161 ---
all0.1633 62099 --
obs0.1633 59066 95.1 %-
Solvent computationBsol: 46.7531 Å2
Displacement parametersBiso max: 49.29 Å2 / Biso mean: 15.1544 Å2 / Biso min: 5.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.222 Å20.241 Å20.521 Å2
2--0.825 Å20.75 Å2
3----1.047 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.66→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 62 432 4426
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_mcbond_it1.2211.5
X-RAY DIFFRACTIONc_scbond_it2.0872
X-RAY DIFFRACTIONc_mcangle_it1.8092
X-RAY DIFFRACTIONc_scangle_it3.0312.5
LS refinement shellResolution: 1.66→1.72 Å
RfactorNum. reflection% reflection
Rfree0.2274 287 -
Rwork0.1836 --
obs-5627 90.6 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ligand.param

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