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- PDB-7c1s: Crystal structure of the starter condensation domain of rhizomide... -

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Basic information

Entry
Database: PDB / ID: 7c1s
TitleCrystal structure of the starter condensation domain of rhizomide synthetase RzmA mutant H140A/R148A in complex with C8-CoA and Leu-SNAC
ComponentsNon-ribosomal peptide synthetase modules
KeywordsBIOSYNTHETIC PROTEIN / nonribosomal peptide synthesis / RzmA-Cs / starter condensation (Cs) domains / C8-CoA / Leu-SNAC
Function / homology
Function and homology information


2,3-dihydroxybenzoate-serine ligase activity / enterobactin synthetase complex / enterobactin biosynthetic process / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / amino acid activation for nonribosomal peptide biosynthetic process / phosphopantetheine binding / cytosol
Similarity search - Function
Nonribosomal peptide synthetase, condensation domain / Polyketide synthase, thioesterase domain / Thioesterase / Chloramphenicol Acetyltransferase / Condensation domain / Condensation domain / Amino acid adenylation domain / Thioesterase / Thioesterase domain / ANL, N-terminal domain ...Nonribosomal peptide synthetase, condensation domain / Polyketide synthase, thioesterase domain / Thioesterase / Chloramphenicol Acetyltransferase / Condensation domain / Condensation domain / Amino acid adenylation domain / Thioesterase / Thioesterase domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-binding enzyme, C-terminal domain superfamily / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
OCTANOYL-COENZYME A / Chem-FGU / Non-ribosomal peptide synthetase modules
Similarity search - Component
Biological speciesParaburkholderia rhizoxinica HKI 454 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.586 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,5453
Polymers48,4191
Non-polymers1,1262
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint7 kcal/mol
Surface area18040 Å2
Unit cell
Length a, b, c (Å)52.828, 72.386, 108.582
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: 48418.785 Da / Num. of mol.: 1 / Mutation: H140V, 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


Mass: 893.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H50N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FGU / S-(2-acetamidoethyl) (2S)-2-azanyl-4-methyl-pentanethioate


Mass: 232.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20N2O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 42.63 %
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: BL19U1 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 31, 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: 2.58→50 Å / Num. obs: 13590 / % possible obs: 99.9 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.044 / Rrim(I) all: 0.158 / Χ2: 0.985 / Net I/σ(I): 4.6 / Num. measured all: 172673
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.58-2.6211.30.7626780.8750.2350.7980.959100
2.62-2.6711.50.7226500.9080.2210.7560.962100
2.67-2.7213.30.6896650.9150.1950.7170.981100
2.72-2.7813.30.6316820.9630.1780.6560.976100
2.78-2.8413.40.5546350.9490.1560.5750.998100
2.84-2.9113.30.4616750.9620.1310.481.01199.9
2.91-2.9813.30.4216730.9690.1190.4381.036100
2.98-3.0613.30.3516620.9750.0990.3651.113100
3.06-3.15130.3096700.980.0890.3221.047100
3.15-3.2513.10.2676660.9830.0760.2781.058100
3.25-3.3712.40.2186720.9890.0640.2281.06299.7
3.37-3.511.30.1686760.9910.0520.1761.071100
3.5-3.6613.70.1576740.9950.0440.1631.023100
3.66-3.8513.50.1286840.9950.0360.1321.014100
3.85-4.0913.30.1056850.9970.030.1090.988100
4.09-4.4113.10.0936820.9970.0260.0960.948100
4.41-4.8512.30.0766900.9970.0220.0790.90299.7
4.85-5.5611.90.0756920.9980.0230.0790.84999.9
5.56-712.90.0767100.9980.0220.0790.821100
7-5011.20.0637690.9980.0190.0660.87499.6

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C1H

7c1h


Resolution: 2.586→30.115 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2524 1347 10 %
Rwork0.1957 12124 -
obs0.2013 13471 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.31 Å2 / Biso mean: 46.0472 Å2 / Biso min: 18.11 Å2
Refinement stepCycle: final / Resolution: 2.586→30.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3387 0 72 82 3541
Biso mean--70.33 38.23 -
Num. residues----433
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5861-2.67850.35931250.2797112494
2.6785-2.78570.33291340.27411207100
2.7857-2.91240.34031320.2571184100
2.9124-3.06580.31811330.24241201100
3.0658-3.25760.29791330.22591196100
3.2576-3.50880.29151350.22251214100
3.5088-3.86130.2191360.17171218100
3.8613-4.41850.21721360.16721223100
4.4185-5.56110.21611380.15831246100
5.5611-30.1150.19921450.16841311100
Refinement TLS params.Method: refined / Origin x: 12.0923 Å / Origin y: 21.923 Å / Origin z: 25.2402 Å
111213212223313233
T0.2406 Å2-0.0029 Å20.025 Å2-0.2055 Å2-0.0007 Å2--0.295 Å2
L1.3753 °2-0.0527 °2-0.3988 °2-1.0608 °2-0.1945 °2--1.9113 °2
S-0.0503 Å °-0.238 Å °-0.0625 Å °0.1469 Å °-0.0282 Å °0.0741 Å °0.0017 Å °0.1342 Å °0.0726 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-2 - 431
2X-RAY DIFFRACTION1allC1
3X-RAY DIFFRACTION1allS1 - 85
4X-RAY DIFFRACTION1allS86 - 90
5X-RAY DIFFRACTION1allB1

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