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- PDB-7c1r: Crystal structure of the starter condensation domain of rhizomide... -

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Basic information

Entry
Database: PDB / ID: 7c1r
TitleCrystal structure of the starter condensation domain of rhizomide synthetase RzmA mutant H140A/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


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-like domain / Chloramphenicol Acetyltransferase / Condensation domain / Condensation domain / Amino acid adenylation domain / Thioesterase / Thioesterase domain ...Nonribosomal peptide synthetase, condensation domain / Polyketide synthase, thioesterase domain / Thioesterase / Chloramphenicol acetyltransferase-like domain / 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 / Non-ribosomal peptide synthetase modules
Similarity search - Component
Biological speciesParaburkholderia rhizoxinica HKI 454 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 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)49,4353
Polymers48,4191
Non-polymers1,0162
Water6,792377
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint11 kcal/mol
Surface area18220 Å2
Unit cell
Length a, b, c (Å)52.767, 72.091, 108.275
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: R148A, H140V
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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


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


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
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: 1.698→50 Å / Num. obs: 46330 / % possible obs: 99.8 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.016 / Rrim(I) all: 0.058 / Χ2: 0.962 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.7310.80.86622580.8730.2680.9090.95999
1.73-1.7611.50.78222930.8980.2360.8190.96199.4
1.76-1.7911.70.68422300.9180.2060.7150.99899.7
1.79-1.8311.60.5623050.9510.1690.5861.0399.5
1.83-1.8712.90.50122700.9670.1430.5211.04699.9
1.87-1.9112.90.40222930.9770.1140.4181.00799.9
1.91-1.9612.90.33722740.9830.0960.3511.00299.9
1.96-2.0212.80.27123040.9860.0780.2831.044100
2.02-2.0712.50.21923060.9920.0640.2281.0299.9
2.07-2.14120.1722800.9930.0510.1781.054100
2.14-2.2211.80.13522910.9940.0410.1421.05199.9
2.22-2.3113.10.12423190.9970.0350.131.048100
2.31-2.4113.10.10223300.9970.0290.1061.034100
2.41-2.5413.20.08422940.9980.0240.0871.005100
2.54-2.7130.06923310.9980.020.0720.977100
2.7-2.9112.30.05623240.9990.0170.0590.963100
2.91-3.213.80.04423480.9990.0120.0460.909100
3.2-3.6613.40.03523590.9990.010.0370.845100
3.66-4.6112.40.027238110.0080.0280.724100
4.61-5012.30.025254010.0070.0260.617100

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Processing

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

7c1h


Resolution: 1.698→36.046 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.12
RfactorNum. reflection% reflection
Rfree0.2291 2000 4.51 %
Rwork0.1861 --
obs0.188 44367 95.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.16 Å2 / Biso mean: 26.097 Å2 / Biso min: 3.83 Å2
Refinement stepCycle: final / Resolution: 1.698→36.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 65 377 3806
Biso mean--39.56 31.79 -
Num. residues----428
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.698-1.74030.27181010.238214369
1.7403-1.78730.25491190.2327251681
1.7873-1.83990.32141330.2467282591
1.8399-1.89930.26811470.2249311299
1.8993-1.96720.28131470.21793117100
1.9672-2.04590.26241480.19983123100
2.0459-2.1390.24071470.19653114100
2.139-2.25180.20431480.18483158100
2.2518-2.39280.23371490.18623146100
2.3928-2.57750.23141490.18573158100
2.5775-2.83680.23151500.19663164100
2.8368-3.24710.21491500.17643199100
3.2471-4.09010.20611530.15353246100
4.0901-36.0460.19981590.165334699
Refinement TLS params.Method: refined / Origin x: 11.5985 Å / Origin y: 21.9208 Å / Origin z: 24.6888 Å
111213212223313233
T0.0854 Å2-0.0076 Å20.0312 Å2-0.0437 Å2-0.001 Å2--0.0844 Å2
L2.0438 °2-0.1471 °2-0.7178 °2-1.13 °20.0783 °2--1.5132 °2
S-0.0446 Å °-0.2608 Å °-0.2078 Å °0.2188 Å °-0.0521 Å °0.0673 Å °0.0207 Å °0.1581 Å °0.0251 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-1 - 431
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 421
4X-RAY DIFFRACTION1allS422 - 459
5X-RAY DIFFRACTION1allC1

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