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- PDB-3mzv: Crystal structure of a decaprenyl diphosphate synthase from Rhodo... -

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Basic information

Entry
Database: PDB / ID: 3mzv
TitleCrystal structure of a decaprenyl diphosphate synthase from Rhodobacter capsulatus
ComponentsDecaprenyl diphosphate synthase
KeywordsTRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


all-trans-octaprenyl-diphosphate synthase / prenyltransferase activity / isoprenoid biosynthetic process
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
Octaprenyl diphosphate synthase
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsQuartararo, C.E. / Patskovsky, Y. / Bonanno, J.B. / Rutter, M. / Bain, K.T. / Chang, S. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.
Authors: Wallrapp, F.H. / Pan, J.J. / Ramamoorthy, G. / Almonacid, D.E. / Hillerich, B.S. / Seidel, R. / Patskovsky, Y. / Babbitt, P.C. / Almo, S.C. / Jacobson, M.P. / Poulter, C.D.
History
DepositionMay 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2013Group: Database references
Revision 1.3Mar 27, 2013Group: Database references
Revision 1.4Apr 24, 2013Group: Database references
Revision 1.5Nov 8, 2017Group: Refinement description / Category: software
Revision 1.6Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.7Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.8Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Decaprenyl diphosphate synthase
B: Decaprenyl diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)74,9612
Polymers74,9612
Non-polymers00
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-31 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.459, 90.245, 80.167
Angle α, β, γ (deg.)90.00, 125.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Decaprenyl diphosphate synthase


Mass: 37480.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07D00
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 294 K / pH: 6.5
Details: 100mM MES pH 6.5, 30% PEG MME 5K, 200mM ammonium sulfate, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97958
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 26, 2010
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 56604 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 13
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3 / Rsym value: 0.479 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.48 / SU ML: 0.1 / SU R Cruickshank DPI: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2837 5.1 %RANDOM
Rwork0.193 ---
obs0.194 56071 99.8 %-
all-56161 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.95 Å2
Baniso -1Baniso -2Baniso -3
1--2.9 Å20 Å2-1.89 Å2
2--1.9 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4795 0 0 305 5100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214893
X-RAY DIFFRACTIONr_bond_other_d0.0020.023209
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9596645
X-RAY DIFFRACTIONr_angle_other_deg1.01237817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0085636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99823.733217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25115803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4521540
X-RAY DIFFRACTIONr_chiral_restr0.0910.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025536
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02982
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_it0.9241.53150
X-RAY DIFFRACTIONr_mcbond_other0.2511.51297
X-RAY DIFFRACTIONr_mcangle_it1.60925004
X-RAY DIFFRACTIONr_scbond_it2.71131743
X-RAY DIFFRACTIONr_scangle_it4.0824.51638
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 179 -
Rwork0.225 3903 -
obs--99.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.41090.16850.20910.7752-0.19141.87720.0649-0.4471-0.07370.241-0.0261-0.1244-0.05120.0249-0.03890.1272-0.02660.00450.13590.01560.092517.77453.6827.375
22.08290.7935-0.31640.4464-0.17740.08640.0083-0.12310.10630.0959-0.0205-0.0035-0.03790.01530.01210.1286-0.03180.01330.04980.01380.091427.68682.7959.368
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 332
2X-RAY DIFFRACTION2B10 - 334

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