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- PDB-7c1u: Crystal structure of the starter condensation domain of rhizomide... -

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Basic information

Entry
Database: PDB / ID: 7c1u
TitleCrystal structure of the starter condensation domain of rhizomide synthetase RzmA mutant H140V/R148A in a "product-released" conformation
ComponentsNon-ribosomal peptide synthetase modules
KeywordsBIOSYNTHETIC PROTEIN / nonribosomal peptide synthesis / RzmA-Cs / starter condensation (Cs) domains
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 / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / 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
Non-ribosomal peptide synthetase modules
Similarity search - Component
Biological speciesParaburkholderia rhizoxinica HKI 454 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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


Theoretical massNumber of molelcules
Total (without water)48,4191
Polymers48,4191
Non-polymers00
Water8,413467
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18940 Å2
Unit cell
Length a, b, c (Å)52.564, 58.784, 134.058
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
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: Jan 9, 2020 / 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: 1.4→50 Å / Num. obs: 80924 / % possible obs: 97.9 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.016 / Rrim(I) all: 0.058 / Χ2: 0.977 / Net I/σ(I): 7.6 / Num. measured all: 1058554
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.4211.80.89737840.8680.260.9360.90592.9
1.42-1.4512.50.85638880.8750.2440.8910.90795.8
1.45-1.48130.70639430.9210.1990.7340.92996.6
1.48-1.5113.30.59539770.940.1670.6180.93396.9
1.51-1.5413.20.52639630.9610.1490.5470.94997.1
1.54-1.5812.50.45939500.960.1340.4790.99897.2
1.58-1.6213.20.35739930.9740.1010.3721.02997.4
1.62-1.6613.80.28839810.9870.0790.2990.98997.7
1.66-1.7113.70.23840130.9890.0660.2480.99397.8
1.71-1.7613.50.19440350.9930.0540.2010.99697.9
1.76-1.83130.16140410.9940.0460.1681.01998.2
1.83-1.912.40.12940510.9960.0380.1341.06898.3
1.9-1.9913.70.140310.9970.0280.1041.07998.5
1.99-2.0913.70.08240910.9980.0230.0851.08198.5
2.09-2.2213.50.0740810.9980.0190.0721.08698.9
2.22-2.3912.60.0641250.9980.0170.0621.06799
2.39-2.6313.50.05241470.9990.0140.0540.97399.3
2.63-3.0213.60.04541540.9990.0130.0470.9299.5
3.02-3.812.60.03942370.9990.0110.040.87699.6
3.8-5012.60.03544390.9990.010.0370.7399.6

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C1H

7c1h


Resolution: 1.4→29.461 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1778 2000 2.62 %
Rwork0.1454 74339 -
obs0.1463 76339 92.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.51 Å2 / Biso mean: 25.932 Å2 / Biso min: 5.23 Å2
Refinement stepCycle: final / Resolution: 1.4→29.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 0 467 3859
Biso mean---34.96 -
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 (%)
1.4-1.43490.212800.174297352
1.4349-1.47370.22221050.1593390869
1.4737-1.5170.18551360.1483503989
1.517-1.5660.22211470.1424547096
1.566-1.62190.17381480.1345552897
1.6219-1.68690.14931510.128557698
1.6869-1.76360.17681490.1274558898
1.7636-1.85660.19731520.1314560098
1.8566-1.97290.18431520.1329566098
1.9729-2.12520.16611520.1343564799
2.1252-2.3390.19551530.141571399
2.339-2.67730.1731550.1526576499
2.6773-3.37230.18171570.15565817100
3.3723-29.4610.16311630.1524605699

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