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- PDB-4lob: Crystal structure of polyprenyl diphosphate synthase A1S_2732 (Ta... -

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Basic information

Entry
Database: PDB / ID: 4lob
TitleCrystal structure of polyprenyl diphosphate synthase A1S_2732 (Target EFI-509223) from Acinetobacter baumannii
ComponentsPolyprenyl synthetase
KeywordsTRANSFERASE / isoprenoid synthase / Enzyme Function Initiative / EFI / Structural Genomics
Function / homologyFarnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Al Obaidi, N. / Stead, M. / Love, J. / Poulter, C.D. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of polyprenyl diphosphate synthase from Acinetobacter baumannii
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Al Obaidi, N. / Stead, M. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Al Obaidi, N. / Stead, M. / Love, J. / Poulter, C.D. / Gerlt, J.A. / Almo, S.C.
History
DepositionJul 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 20, 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 / 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 / _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

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Assembly

Deposited unit
A: Polyprenyl synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4025
Polymers38,2031
Non-polymers1984
Water1,56787
1
A: Polyprenyl synthetase
hetero molecules

A: Polyprenyl synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,80410
Polymers76,4072
Non-polymers3978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
Buried area5020 Å2
ΔGint-91 kcal/mol
Surface area26180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.245, 46.008, 49.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Polyprenyl synthetase / polyprenyl synthase


Mass: 38203.375 Da / Num. of mol.: 1 / Fragment: UNP residues 23-347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ACINIS123_1931 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
References: UniProt: J4JED5, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.5 M potassium thiocyanate, pH 4.5, 0.1 M sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 6, 2013 / Details: mirrors
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 23096 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rsym value: 0.13 / Net I/σ(I): 6.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.7 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JYX

4jyx


Resolution: 2→30.5 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 12.463 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26609 745 3.2 %RANDOM
Rwork0.20038 ---
obs0.20231 22212 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.628 Å2
Baniso -1Baniso -2Baniso -3
1--3.73 Å20 Å20 Å2
2--5.31 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 2→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 9 87 2590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192593
X-RAY DIFFRACTIONr_bond_other_d0.0010.022523
X-RAY DIFFRACTIONr_angle_refined_deg0.9581.9693522
X-RAY DIFFRACTIONr_angle_other_deg0.72535794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.785336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34224.872117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84115451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4861516
X-RAY DIFFRACTIONr_chiral_restr0.0490.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022970
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.0343.191326
X-RAY DIFFRACTIONr_mcbond_other10.0373.1881325
X-RAY DIFFRACTIONr_mcangle_it11.5955.3061659
X-RAY DIFFRACTIONr_mcangle_other11.5925.3091660
X-RAY DIFFRACTIONr_scbond_it11.9113.7941267
X-RAY DIFFRACTIONr_scbond_other11.9113.7941267
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.3535.9751861
X-RAY DIFFRACTIONr_long_range_B_refined14.9114.5543065
X-RAY DIFFRACTIONr_long_range_B_other14.92914.5633066
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 57 -
Rwork0.304 1610 -
obs--99.58 %
Refinement TLS params.Method: refined / Origin x: 163.1512 Å / Origin y: 48.0596 Å / Origin z: 4.8267 Å
111213212223313233
T0.17 Å2-0.0082 Å20.0222 Å2-0.0449 Å2-0.047 Å2--0.1594 Å2
L2.576 °2-0.3605 °20.7983 °2-1.0373 °2-0.7106 °2--2.3898 °2
S-0.0735 Å °-0.2876 Å °0.2298 Å °0.1418 Å °0.0557 Å °0.0565 Å °-0.1715 Å °-0.2015 Å °0.0178 Å °

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