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- PDB-3zmc: Native structure of Farnesyl Pyrophosphate Synthase from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 3zmc
TitleNative structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound substrate molecule Geranyl pyrophosphate.
ComponentsGERANYLTRANSTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
: / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GERANYL DIPHOSPHATE / Geranyltranstransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.87 Å
AuthorsSchmidberger, J.W. / Schnell, R. / Schneider, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural Characterization of Substrate and Inhibitor Binding to Farnesyl Pyrophosphate Synthase from Pseudomonas Aeruginosa
Authors: Schmidberger, J.W. / Schnell, R. / Schneider, G.
History
DepositionFeb 7, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_atom_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_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_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_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: GERANYLTRANSTRANSFERASE
B: GERANYLTRANSTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,09811
Polymers63,1782
Non-polymers9209
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-69.4 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.963, 98.778, 130.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2171-

HOH

21B-2007-

HOH

31B-2011-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.2188, -0.9655, -0.1415), (-0.9645, 0.192, 0.1814), (-0.148, 0.1762, -0.9732)
Vector: 53.03, 48.49, -36.79)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GERANYLTRANSTRANSFERASE / PA4043


Mass: 31588.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q9HWY4, (2E,6E)-farnesyl diphosphate synthase

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Non-polymers , 5 types, 425 molecules

#2: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O7P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHERE IS AN N-TERMINAL ADDITIONAL SERINE RESULTING FROM CLONING AND CLEAVAGE OF HIS TAG.

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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: 2.21 Å3/Da / Density % sol: 44.28 %
Description: DATA IS SUBSTRATE COMPLEX, SOLVED BY REFINING AGAINST NATIVE MODEL USING NATIVE FREER FLAGS.
Crystal growpH: 8 / Details: 0.15 M MGCL2, 20% PEG8000, 0.1 M TRISCL PH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97626
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.87→40.83 Å / Num. obs: 46143 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.2
Reflection shellResolution: 1.87→1.91 Å / Redundancy: 5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: SIR
Starting model: PDB ENTRY 3ZCD

3zcd


Resolution: 1.87→40.86 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.889 / SU B: 3.581 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 2275 4.9 %RANDOM
Rwork0.20489 ---
obs0.20711 43687 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.409 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20 Å2
2---0.75 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.87→40.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4068 0 53 416 4537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194189
X-RAY DIFFRACTIONr_bond_other_d0.0070.024097
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.9925679
X-RAY DIFFRACTIONr_angle_other_deg1.28639345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1455543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.54222.872188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92615661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6181547
X-RAY DIFFRACTIONr_chiral_restr0.1110.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214817
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02938
X-RAY DIFFRACTIONr_nbd_refined0.2740.21573
X-RAY DIFFRACTIONr_nbd_other0.2150.23531
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22122
X-RAY DIFFRACTIONr_nbtor_other0.0990.22257
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.286
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0880.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.536 175 -
Rwork0.505 3117 -
obs--98.71 %

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