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- PDB-3zl6: Native structure of Farnesyl Pyrophosphate Synthase from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 3zl6
TitleNative structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PAO1, with bound fragment KM10833.
ComponentsGERANYLTRANSTRANSFERASE
KeywordsTRANSFERASE / KM10833 / MAYBRIDGE FRAGMENT LIBRARY
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
2-(1,2-benzoxazol-3-yl)ethanoic acid / Geranyltranstransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.85 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
DepositionJan 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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)63,7619
Polymers63,1782
Non-polymers5837
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-48.4 kcal/mol
Surface area21470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.160, 98.840, 131.550
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-2180-

HOH

21B-2009-

HOH

31B-2012-

HOH

41B-2198-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.2177, -0.9637, -0.1544), (-0.965, 0.1888, 0.1819), (-0.1461, 0.1886, -0.9711)
Vector: 52.44, 48.43, -37.69)

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Components

#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
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NVU / 2-(1,2-benzoxazol-3-yl)ethanoic acid


Mass: 177.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details(1,2-BENZISOXAZOL-3-YL)ACETIC ACID (NVU): FRAGMENT FROM MAYBRIDGE LIBRARY KM10833
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: 2.31 Å3/Da / Density % sol: 46.7 % / Description: NONE
Crystal growpH: 8 / Details: 0.2 M MGCL2, 20% PEG6000, 0.1 M TRISCL PH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.00319
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00319 Å / Relative weight: 1
ReflectionResolution: 1.85→32.26 Å / Num. obs: 47364 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

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

3zcd


Resolution: 1.85→31.35 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.929 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22222 2339 5 %RANDOM
Rwork0.17545 ---
obs0.17774 44882 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2---0.85 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.85→31.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 37 429 4552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194188
X-RAY DIFFRACTIONr_bond_other_d0.0070.024074
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.995676
X-RAY DIFFRACTIONr_angle_other_deg1.2763.0019295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1465544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40522.979188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08515660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1731546
X-RAY DIFFRACTIONr_chiral_restr0.1090.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214838
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02940
X-RAY DIFFRACTIONr_nbd_refined0.2670.21559
X-RAY DIFFRACTIONr_nbd_other0.2220.23400
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22113
X-RAY DIFFRACTIONr_nbtor_other0.10.22193
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0760.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3420.250
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.25
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: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 182 -
Rwork0.253 3289 -
obs--99.66 %

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