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

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Basic information

Entry
Database: PDB / ID: 3zmb
TitleNative structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound fragment SPB02696.
ComponentsGERANYLTRANSTRANSFERASE
KeywordsTRANSFERASE / MAYBRIDGE FRAGMENT LIBRARY
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process / metal ion binding
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
3-(2-oxo-1,3-benzoxazol-3(2H)-yl)propanoic acid / Geranyltranstransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.9 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 / 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 / _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)63,9137
Polymers63,1782
Non-polymers7355
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-39.3 kcal/mol
Surface area21490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.560, 98.840, 131.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.2138, -0.9645, -0.1549), (-0.9651, 0.184, 0.1861), (-0.151, 0.1893, -0.9702)
Vector: 52.62, 48.9, -37.57)

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Components

#1: Protein GERANYLTRANSTRANSFERASE / / FARNESYL PYROPHOSPHATE SYNTHASE


Mass: 31588.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FRAGMENT COMPLEX WITH SPB02696. / 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-6H6 / 3-(2-oxo-1,3-benzoxazol-3(2H)-yl)propanoic acid


Mass: 207.183 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H9NO4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details3-(2-OXO-1,3-BENZOXAZOL-3(2H)-YL)PROPANOIC ACID (6H6): SPB02696 IS A FRAGMENT FROM THE MAYBRIDGE ...3-(2-OXO-1,3-BENZOXAZOL-3(2H)-YL)PROPANOIC ACID (6H6): SPB02696 IS A FRAGMENT FROM THE MAYBRIDGE FRAGMENT LIBRARY.
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: 44.46 %
Description: DATA IS A FRAGMENT COMPLEX DATA SET REFINED AGAINST ORIGINAL FREE R FLAGS OF NATIVE STRUCTURE.
Crystal growpH: 8 / Details: 0.2 M MGCL2, 20% PEG6000, 0.1 M TRIS 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: 1.9→32.88 Å / Num. obs: 43864 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.9 / % possible all: 99.5

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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: 1.9→32.9 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.895 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 165 TO 166 OF A CHAIN MISSING (DISORDERED). RESIDUES 229 TO 241 OF BOTH A AND B CHAINS MISSING (DISORDERED LOOP).
RfactorNum. reflection% reflectionSelection details
Rfree0.24095 2196 5 %RANDOM
Rwork0.18849 ---
obs0.19114 41464 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.275 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2---1.11 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 50 609 4763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194250
X-RAY DIFFRACTIONr_bond_other_d0.0060.024127
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9945769
X-RAY DIFFRACTIONr_angle_other_deg1.1773.0019400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4725556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99323.089191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27615675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3861546
X-RAY DIFFRACTIONr_chiral_restr0.0970.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214909
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02938
X-RAY DIFFRACTIONr_nbd_refined0.2780.21806
X-RAY DIFFRACTIONr_nbd_other0.2190.23562
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22131
X-RAY DIFFRACTIONr_nbtor_other0.1010.22244
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.292
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2420.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3250.255
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.23
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 174 -
Rwork0.444 3025 -
obs--99.32 %

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