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- PDB-6ime: Rv2361c complex with substrate analogues -

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Basic information

Entry
Database: PDB / ID: 6ime
TitleRv2361c complex with substrate analogues
ComponentsDecaprenyl diphosphate synthase
KeywordsTRANSFERASE / decaprenyl diphosphate synthesis / substrate binding mode / catalytic mechanism / rossmann-like fold / butterfly
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] / dehydrodolichyl diphosphate synthase activity / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / Z-farnesyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase 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] / dehydrodolichyl diphosphate synthase activity / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / Z-farnesyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase 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
CARBONATE ION / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / GERANYL S-THIOLODIPHOSPHATE / Chem-ISY / Decaprenyl diphosphate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKo, T.-P. / Guo, R.-T. / Chen, C.-C. / Liu, W.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-KPQ-105-TPP Taiwan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase.
Authors: Ko, T.-P. / Xiao, X. / Guo, R.-T. / Huang, J.-W. / Liu, W. / Chen, C.-C.
History
DepositionOct 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,99211
Polymers67,6792
Non-polymers1,3139
Water13,097727
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-38 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.711, 89.120, 94.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Decaprenyl diphosphate synthase / DecaPP / Decaprenyl pyrophosphate synthase / Long-chain isoprenyl diphosphate synthase / Trans / ...DecaPP / Decaprenyl pyrophosphate synthase / Long-chain isoprenyl diphosphate synthase / Trans / polycis-decaprenyl diphosphate synthase


Mass: 33839.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: uppS, Rv2361c, MTCY27.19 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WFF7, trans,polycis-decaprenyl diphosphate synthase, ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific]

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Non-polymers , 8 types, 736 molecules

#2: Chemical ChemComp-GST / GERANYL S-THIOLODIPHOSPHATE / S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE


Mass: 330.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H20O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: CO3
#6: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O2S2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-ISY / 3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid / Isopentyl S-Thiolodiphosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 727 / 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: 2.52 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 10% GLYCEROL, 25% PEG 400, 7% PEG 3000, 1mM ISPP, 1mM GSPP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→25 Å / Num. obs: 95419 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.016 / Net I/σ(I): 48.7
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 9410 / CC1/2: 0.981 / Rpim(I) all: 0.186 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ONC

4onc


Resolution: 1.55→24.411 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.167 2008 2.11 %
Rwork0.1454 --
obs0.1458 95335 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→24.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4592 0 73 727 5392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134895
X-RAY DIFFRACTIONf_angle_d1.3476646
X-RAY DIFFRACTIONf_dihedral_angle_d16.7462950
X-RAY DIFFRACTIONf_chiral_restr0.08678
X-RAY DIFFRACTIONf_plane_restr0.009875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58870.20591330.18736461X-RAY DIFFRACTION98
1.5887-1.63170.1931480.17336594X-RAY DIFFRACTION100
1.6317-1.67970.18061430.15986592X-RAY DIFFRACTION100
1.6797-1.73390.19681450.15756614X-RAY DIFFRACTION100
1.7339-1.79580.16781470.14976631X-RAY DIFFRACTION100
1.7958-1.86770.1711300.14946635X-RAY DIFFRACTION100
1.8677-1.95270.15791460.14146618X-RAY DIFFRACTION100
1.9527-2.05560.16411410.1346678X-RAY DIFFRACTION100
2.0556-2.18430.16651510.13846674X-RAY DIFFRACTION100
2.1843-2.35280.17161370.1396687X-RAY DIFFRACTION100
2.3528-2.58930.17481490.14746677X-RAY DIFFRACTION100
2.5893-2.96340.18481430.14556757X-RAY DIFFRACTION100
2.9634-3.73150.15461430.13456784X-RAY DIFFRACTION100
3.7315-24.41360.15471520.15016925X-RAY DIFFRACTION99
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)
11.04490.01840.10080.5144-0.5190.6338-0.0362-0.1912-0.00370.07160.02160.0546-0.05730.01180.00020.15150.02820.01210.1948-0.00610.105436.681224.311660.6748
20.67420.4072-0.02170.5246-0.40680.6403-0.0527-0.0284-0.0522-0.02140.07620.10030.0802-0.07180.00450.14670.01720.03670.16430.01160.169822.700921.140251.2086
30.4145-0.16390.29760.2178-0.37340.8532-0.0431-0.00360.10610.0290.0278-0.0198-0.07110.02180.00370.14890.00530.00670.14580.00610.160329.803933.606741.7975
40.49930.18780.03570.7447-0.55510.6688-0.01410.01570.0164-0.0949-0.1292-0.22120.00510.1139-0.07890.1458-0.00870.03330.14330.03090.18952.90336.299517.0628
50.30810.02160.040.6605-0.20170.1982-0.02060.08380.0649-0.03350.01310.0332-0.0303-0.027700.1646-0.00360.00850.14330.01640.156137.860644.75117.8276
60.25380.0568-0.40180.2039-0.19760.2894-0.01910.04-0.0167-0.01050.0112-0.02930.0211-0.01490.00490.139-0.0134-0.00190.13680.00530.146634.047531.599727.7676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 110 )
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 196 )
3X-RAY DIFFRACTION3chain 'A' and (resid 197 through 296 )
4X-RAY DIFFRACTION4chain 'B' and (resid 12 through 110 )
5X-RAY DIFFRACTION5chain 'B' and (resid 111 through 196 )
6X-RAY DIFFRACTION6chain 'B' and (resid 197 through 296 )

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