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- PDB-2vg4: Rv2361 native -

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Basic information

Entry
Database: PDB / ID: 2vg4
TitleRv2361 native
ComponentsUNDECAPRENYL PYROPHOSPHATE SYNTHETASE
KeywordsTRANSFERASE / PRENYLTRANSFERASE / PEPTIDOGLYCAN SYNTHESIS / CELL WALL BIOGENESIS/DEGRADATION / CELL CYCLE / CELL SHAPE / CELL DIVISION
Function / homology
Function and homology information


trans,polycis-decaprenyl diphosphate synthase / all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / Z-farnesyl diphosphate synthase activity / dehydrodolichyl diphosphate synthase activity / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / polyprenol biosynthetic process / prenyltransferase activity / manganese ion binding / magnesium ion binding ...trans,polycis-decaprenyl diphosphate synthase / all-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] / Z-farnesyl diphosphate synthase activity / dehydrodolichyl diphosphate synthase activity / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / polyprenol biosynthetic process / prenyltransferase activity / manganese ion binding / magnesium ion binding / plasma membrane / cytosol
Similarity search - Function
Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Decaprenyl diphosphate synthase / Decaprenyl diphosphate synthase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.6 Å
AuthorsNaismith, J.H. / Wang, W. / Dong, C.
CitationJournal: J. Mol. Biol. / Year: 2008
Title: The structural basis of chain length control in Rv1086.
Authors: Wang, W. / Dong, C. / McNeil, M. / Kaur, D. / Mahapatra, S. / Crick, D.C. / Naismith, J.H.
History
DepositionNov 8, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 18, 2017Group: Atomic model / Data collection / Derived calculations
Category: atom_site / diffrn ...atom_site / diffrn / diffrn_radiation_wavelength / diffrn_source / pdbx_struct_sheet_hbond / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id
Revision 2.1Dec 13, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.2Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 2.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
B: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
C: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
D: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)129,8434
Polymers129,8434
Non-polymers00
Water27015
1
A: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
C: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)64,9222
Polymers64,9222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-10.08 kcal/mol
Surface area24190 Å2
MethodPISA
2
B: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
D: UNDECAPRENYL PYROPHOSPHATE SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)64,9222
Polymers64,9222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-11.74 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.300, 87.300, 183.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
UNDECAPRENYL PYROPHOSPHATE SYNTHETASE / UPP SYNTHETASE / DI-TRANS / POLY-CIS-DECAPRENYL CISTRANSFERASE / UNDECAPRENYL DIPHOSPHATE SYNTHASE ...UPP SYNTHETASE / DI-TRANS / POLY-CIS-DECAPRENYL CISTRANSFERASE / UNDECAPRENYL DIPHOSPHATE SYNTHASE / UDS / RV2361C


Mass: 32460.809 Da / Num. of mol.: 4 / Fragment: RESIDUES 13-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: P60479, UniProt: P9WFF7*PLUS, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.86 Å3/Da / Density % sol: 56.7 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 / Wavelength: 0.933 Å
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→69 Å / Num. obs: 44230 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.6→52 Å / Stereochemistry target values: ML
Details: THE TWIN FRACTION WAS REFINED THROUGHOUT. THE TWINNING OPERATOR IS -H-K,K,-L. TWINNING FRACTION IS NOT KNOWN. BOTH TWINNED AND DE-TWINNED DATASETS ARE AVAILABLE UNDER THE CODE R2VG4SF.ENT.
RfactorNum. reflection% reflection
Rfree0.255 -5 %
Rwork0.216 --
obs0.23 44230 84 %
Refinement stepCycle: LAST / Resolution: 2.6→52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9141 0 0 15 9156

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