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- PDB-6p1j: The structure of condensation and adenylation domains of teixobac... -

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Basic information

Entry
Database: PDB / ID: 6p1j
TitleThe structure of condensation and adenylation domains of teixobactin-producing nonribosomal peptide synthetase Txo2 serine module
ComponentsTxo2
KeywordsBIOSYNTHETIC PROTEIN / Nonribosomal peptide synthetase / Teixobactin / Txo2 / Condensation domain / Adenylation domain / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / biosynthetic process / phosphopantetheine binding
Similarity search - Function
Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain ...Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
ACETATE ION / CITRATE ANION / FORMIC ACID / Txo2
Similarity search - Component
Biological speciesEleftheria terrae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsTan, K. / Zhou, M. / Jedrzejczak, R. / Babnigg, G. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Curr Res Struct Biol / Year: 2020
Title: Structures of teixobactin-producing nonribosomal peptide synthetase condensation and adenylation domains.
Authors: Tan, K. / Zhou, M. / Jedrzejczak, R.P. / Wu, R. / Higuera, R.A. / Borek, D. / Babnigg, G. / Joachimiak, A.
History
DepositionMay 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Txo2
B: Txo2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,21036
Polymers212,2162
Non-polymers1,99434
Water1,38777
1
A: Txo2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,26717
Polymers106,1081
Non-polymers1,15916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Txo2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,94219
Polymers106,1081
Non-polymers83418
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.857, 399.875, 144.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1111-

CL

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Txo2


Mass: 106108.008 Da / Num. of mol.: 2
Fragment: condensation and adenylation domains (UNP residues 45-1005)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eleftheria terrae (bacteria) / Plasmid: pMCSG68 / Cell (production host): pGro7-K / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B5H0S3

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Non-polymers , 7 types, 111 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.76 Å3/Da / Density % sol: 67.31 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium citrate, 0.1 M Tris-HCl, 15% v/v PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9717 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 2.95→47.2 Å / Num. obs: 66302 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 54.1 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.069 / Rrim(I) all: 0.132 / Χ2: 1.214 / Net I/σ(I): 10.6
Reflection shellResolution: 2.95→3.04 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5527 / CC1/2: 0.71 / Rpim(I) all: 0.535 / Rrim(I) all: 0.999 / Χ2: 0.994 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6OYF

6oyf


Resolution: 2.95→47.2 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.23
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 3241 4.9 %random
Rwork0.2263 ---
obs0.2283 66102 97.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.95→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14852 0 104 77 15033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215283
X-RAY DIFFRACTIONf_angle_d0.45820798
X-RAY DIFFRACTIONf_dihedral_angle_d15.9169196
X-RAY DIFFRACTIONf_chiral_restr0.0382272
X-RAY DIFFRACTIONf_plane_restr0.0042776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-2.9940.35491430.34212652X-RAY DIFFRACTION96
2.994-3.04080.40851530.32942733X-RAY DIFFRACTION99
3.0408-3.09070.35481520.32812733X-RAY DIFFRACTION98
3.0907-3.1440.32241200.31642753X-RAY DIFFRACTION99
3.144-3.20110.36081270.30672722X-RAY DIFFRACTION99
3.2011-3.26270.33951460.30022748X-RAY DIFFRACTION98
3.2627-3.32920.31741520.27982709X-RAY DIFFRACTION99
3.3292-3.40160.28831370.27732735X-RAY DIFFRACTION99
3.4016-3.48070.41151540.27972701X-RAY DIFFRACTION98
3.4807-3.56770.30441540.25512744X-RAY DIFFRACTION99
3.5677-3.66420.30061570.25582703X-RAY DIFFRACTION98
3.6642-3.7720.30411380.24672725X-RAY DIFFRACTION98
3.772-3.89370.27681260.23732716X-RAY DIFFRACTION98
3.8937-4.03280.2911430.2272737X-RAY DIFFRACTION98
4.0328-4.19410.22611410.19192733X-RAY DIFFRACTION98
4.1941-4.38490.21951340.19352746X-RAY DIFFRACTION98
4.3849-4.61590.26971180.18452787X-RAY DIFFRACTION98
4.6159-4.90490.23391530.18022729X-RAY DIFFRACTION98
4.9049-5.28310.19911270.1792761X-RAY DIFFRACTION97
5.2831-5.8140.22321450.1942748X-RAY DIFFRACTION97
5.814-6.65350.23951510.20942728X-RAY DIFFRACTION96
6.6535-8.37560.19451390.18782753X-RAY DIFFRACTION96
8.3756-48.48230.20551310.18142765X-RAY DIFFRACTION92
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)
12.6039-1.0575-0.06223.29770.75544.2527-0.38240.39570.38170.0167-0.11040.0882-0.6873-0.61810.48120.5802-0.0596-0.31240.598-0.08090.505532.5705101.84698.0194
21.40070.1894-0.17121.5443-0.6971.929-0.08610.1295-0.1146-0.015-0.03460.0824-0.25980.01870.13380.41450.0239-0.22310.3817-0.07480.478743.973687.958725.6261
31.2381-0.5774-0.57441.325-0.83581.32950.16550.2271-0.3184-0.2182-0.0250.6592-0.2698-0.7457-0.10750.5380.134-0.24420.5238-0.07490.645328.393885.455127.6714
40.55740.96590.0614.7825-0.32210.3420.11850.0387-0.44010.4458-0.04060.46380.1318-0.1405-0.07460.5251-0.08050.01290.5027-0.02370.929833.391930.330450.1649
50.95750.2579-0.09282.0475-0.27511.07070.07670.5113-0.318-0.1784-0.07860.45730.3281-0.22690.02420.453-0.0976-0.11740.6025-0.08511.013228.988736.674732.6963
61.0465-0.1521-0.98151.8035-0.5723.05420.15290.1842-0.2301-0.1266-0.11760.09330.06790.08590.00120.371-0.0155-0.15990.4712-0.02850.718842.978650.443529.1968
71.73180.33790.96051.13660.81661.681-0.2244-0.29840.20030.02020.05250.029-0.26470.02010.14030.51790.0525-0.18040.3979-0.04730.415217.226577.9094-18.3688
80.6579-0.17290.0513.01250.46520.5657-0.0067-0.1873-0.39330.00030.0681-0.46170.13990.0925-0.06890.41990.0924-0.08670.51080.03410.874524.683224.5523-40.0632
90.97960.6755-0.95532.13810.19772.2940.1254-0.3013-0.05460.2345-0.1287-0.14880.02220.0174-0.04070.46850.0571-0.16420.51210.00930.824213.137934.9527-30.3552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 198 )
2X-RAY DIFFRACTION2chain 'A' and (resid 199 through 393 )
3X-RAY DIFFRACTION3chain 'A' and (resid 394 through 472 )
4X-RAY DIFFRACTION4chain 'A' and (resid 473 through 669 )
5X-RAY DIFFRACTION5chain 'A' and (resid 670 through 851 )
6X-RAY DIFFRACTION6chain 'A' and (resid 852 through 1005 )
7X-RAY DIFFRACTION7chain 'B' and (resid 44 through 393 )
8X-RAY DIFFRACTION8chain 'B' and (resid 394 through 838 )
9X-RAY DIFFRACTION9chain 'B' and (resid 839 through 1005 )

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