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- PDB-7c1l: Crystal structure of the starter condensation domain of rhizomide... -

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Basic information

Entry
Database: PDB / ID: 7c1l
TitleCrystal structure of the starter condensation domain of rhizomide synthetase RzmA mutant R148A in complex with C8-CoA
ComponentsNon-ribosomal peptide synthetase modules
KeywordsBIOSYNTHETIC PROTEIN / nonribosomal peptide synthesis / RzmA-Cs / starter condensation (Cs) domains / C8-CoA
Function / homology
Function and homology information


Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / : / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / carboxylic acid metabolic process / phosphopantetheine binding / ligase activity / cytosol
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, C-terminal domain superfamily / 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
OCTANOYL-COENZYME A / Non-ribosomal peptide synthetase modules
Similarity search - Component
Biological speciesParaburkholderia rhizoxinica HKI 454 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZhong, L. / Diao, X. / Zhang, N. / Li, F.W. / Zhou, H.B. / Chen, H.N. / Ren, X. / Zhang, Y. / Wu, D. / Bian, X.
CitationJournal: Nat Commun / Year: 2021
Title: Engineering and elucidation of the lipoinitiation process in nonribosomal peptide biosynthesis.
Authors: Zhong, L. / Diao, X. / Zhang, N. / Li, F. / Zhou, H. / Chen, H. / Bai, X. / Ren, X. / Zhang, Y. / Wu, D. / Bian, X.
History
DepositionMay 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 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

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Assembly

Deposited unit
A: Non-ribosomal peptide synthetase modules
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4743
Polymers48,4581
Non-polymers1,0162
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint10 kcal/mol
Surface area17980 Å2
Unit cell
Length a, b, c (Å)52.907, 72.331, 108.543
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Non-ribosomal peptide synthetase modules


Mass: 48457.801 Da / Num. of mol.: 1 / Mutation: R148A
Source method: isolated from a genetically manipulated source
Details: rhizomide synthetase RzmA
Source: (gene. exp.) Paraburkholderia rhizoxinica HKI 454 (bacteria)
Strain: HKI 454 / Gene: RBRH_01504 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: E5ATN9, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-CO8 / OCTANOYL-COENZYME A / Octanoyl-CoA


Mass: 893.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H50N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: BIS-TRIS propane, PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2019 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.847→60.19 Å / Num. obs: 36483 / % possible obs: 99.8 % / Redundancy: 12.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.02 / Rrim(I) all: 0.071 / Net I/σ(I): 17.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.959.10.5324717451950.9740.1820.5632.898.7
5.84-60.1911.40.0451483113010.9990.0140.04741.599.9

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIX1.14phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C1H

7c1h


Resolution: 1.85→26.454 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.96
RfactorNum. reflection% reflection
Rfree0.2283 1971 5.48 %
Rwork0.1909 --
obs0.193 35982 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.04 Å2 / Biso mean: 54.5426 Å2 / Biso min: 18.95 Å2
Refinement stepCycle: final / Resolution: 1.85→26.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 65 163 3619
Biso mean--67.29 44.67 -
Num. residues----432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.89330.33911270.2751224592
1.8933-1.94450.29921370.2487233396
1.9445-2.00170.36141350.2429234998
2.0017-2.06620.27031370.2398238198
2.0662-2.14010.30671410.2298240999
2.1401-2.22570.2911390.2175240099
2.2257-2.32690.2411420.22462447100
2.3269-2.44950.26571400.22062415100
2.4495-2.60290.30241430.22732449100
2.6029-2.80370.29451430.23132477100
2.8037-3.08540.26961430.2242474100
3.0854-3.5310.22231440.1962481100
3.531-4.44520.19581460.15392515100
4.4452-26.4540.15591540.14612636100
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)
13.6029-0.1135-1.25031.32790.48741.66520.06070.3978-0.23810.0154-0.13560.3926-0.0133-0.36170.05450.24430.0220.0050.2847-0.05190.3290.330723.793715.1697
23.83840.8225-1.3791.82430.08443.34930.11040.45560.0162-0.0317-0.06740.1551-0.1749-0.2212-0.05390.190.04420.01490.2264-0.02470.234710.072925.28659.9887
31.939-1.4865-1.34551.76631.69063.4171-0.56020.3151-1.37120.1488-0.00260.85050.698-0.43670.93340.4742-0.09270.13560.2952-0.1771.0338-0.43399.005618.4018
44.13053.6726-1.94347.4297-2.46592.7033-0.151-1.9548-0.15040.9426-0.01430.7135-0.15470.45680.01530.56830.22410.2640.88910.32080.56666.627424.24240.8475
52.6439-0.2002-1.1231.85190.19973.2239-0.2652-1.1235-0.47580.5543-0.0439-0.28190.50930.89050.16250.4820.1244-0.01070.71130.18070.388518.780517.410537.3683
69.08392.5741-0.33686.57470.01484.0543-0.2205-0.65760.42940.51380.06330.7526-0.4722-0.55630.11860.55280.17810.20140.66350.16310.57042.181123.79540.3713
73.24990.3614-0.76671.21120.60133.96760.0166-0.854-0.24020.340.0861-0.3246-0.01131.1014-0.13250.3115-0.0231-0.02980.57840.01950.378624.408824.499729.3931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 70 )A-1 - 70
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 164 )A71 - 164
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 188 )A165 - 188
4X-RAY DIFFRACTION4chain 'A' and (resid 189 through 223 )A189 - 223
5X-RAY DIFFRACTION5chain 'A' and (resid 224 through 319 )A224 - 319
6X-RAY DIFFRACTION6chain 'A' and (resid 320 through 341 )A320 - 341
7X-RAY DIFFRACTION7chain 'A' and (resid 342 through 430 )A342 - 430

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