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- PDB-1f75: CRYSTAL STRUCTURE OF UNDECAPRENYL DIPHOSPHATE SYNTHASE FROM MICRO... -

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Basic information

Entry
Database: PDB / ID: 1f75
TitleCRYSTAL STRUCTURE OF UNDECAPRENYL DIPHOSPHATE SYNTHASE FROM MICROCOCCUS LUTEUS B-P 26
ComponentsUNDECAPRENYL PYROPHOSPHATE SYNTHETASE
KeywordsTRANSFERASE / PARALLEL BETA SHEET / new fold for Isoprenoid Synthase / PEPTIDOGLYCAN SYNTHESIS
Function / homology
Function and homology information


ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity / polyprenol biosynthetic process / manganese ion binding / magnesium ion binding / cytosol
Similarity search - Function
Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
Similarity search - Component
Biological speciesMicrococcus luteus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å
AuthorsFujihashi, M. / Zhang, Y.-W. / Higuchi, Y. / Li, X.-Y. / Koyama, T. / Miki, K.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase.
Authors: Fujihashi, M. / Zhang, Y.W. / Higuchi, Y. / Li, X.Y. / Koyama, T. / Miki, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and preliminary X-ray diffraction studies of undecaprenyl diphosphate synthase from Micrococcus luteus B-P 26
Authors: Fujihashi, M. / Shimizu, N. / Zhang, Y.W. / Koyama, T. / Miki, K.
History
DepositionJun 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
B: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0834
Polymers57,8902
Non-polymers1922
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-49 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.197, 60.161, 75.703
Angle α, β, γ (deg.)90.00, 105.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein UNDECAPRENYL PYROPHOSPHATE SYNTHETASE


Mass: 28945.227 Da / Num. of mol.: 2 / Mutation: K54R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micrococcus luteus (bacteria) / Plasmid: PMLUEX3 / Production host: Escherichia coli (E. coli)
References: UniProt: O82827, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.4
Details: ammonium sulfate, lithium sulfate, pH 5.4, VAPOR DIFFUSION, temperature 293.0K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
220 mMTris-HCl1drop
3100 mM1dropNaCl
41 mMdithiothreitol1drop
50.1 Msodium citrate1reservoir
60.5 Mammonium sulfate1reservoir
71.0 Mlithium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 10 / Num. obs: 57323 / % possible obs: 83.7 % / Observed criterion σ(I): 1 / Redundancy: 2.43 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 24.3
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.168 / % possible all: 56.8
Reflection
*PLUS
Num. obs: 23530 / Num. measured all: 57323
Reflection shell
*PLUS
% possible obs: 56.8 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.246 1252 Random
Rwork0.19 --
all-24741 -
obs-23489 -
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 0 10 38 3552
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.12
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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