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- PDB-7c1p: Crystal structure of the starter condensation domain of the rhizo... -

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Basic information

Entry
Database: PDB / ID: 7c1p
TitleCrystal structure of the starter condensation domain of the rhizomide synthetase RzmA mutant H140V, R148A
ComponentsNon-ribosomal peptide synthetase modules
KeywordsBIOSYNTHETIC PROTEIN / nonribosomal peptide synthesis / RzmA / 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-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 / Chloramphenicol acetyltransferase-like domain superfamily / 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: 2.6 Å
AuthorsZhong, L. / Diao, X. / Zhang, N. / Li, F.W. / Zhou, H.B. / Chen, H.N. / Ren, X. / Zhang, Y. / Wu, D.
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
B: Non-ribosomal peptide synthetase modules
C: Non-ribosomal peptide synthetase modules
D: Non-ribosomal peptide synthetase modules


Theoretical massNumber of molelcules
Total (without water)193,6754
Polymers193,6754
Non-polymers00
Water5,801322
1
A: Non-ribosomal peptide synthetase modules


Theoretical massNumber of molelcules
Total (without water)48,4191
Polymers48,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-ribosomal peptide synthetase modules


Theoretical massNumber of molelcules
Total (without water)48,4191
Polymers48,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-ribosomal peptide synthetase modules


Theoretical massNumber of molelcules
Total (without water)48,4191
Polymers48,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Non-ribosomal peptide synthetase modules


Theoretical massNumber of molelcules
Total (without water)48,4191
Polymers48,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.636, 89.651, 98.067
Angle α, β, γ (deg.)66.890, 90.020, 90.250
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Non-ribosomal peptide synthetase modules


Mass: 48418.785 Da / Num. of mol.: 4 / Mutation: H140V, R148A
Source method: isolated from a genetically manipulated source
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.: 322 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Description: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: Citric acid, BIS-TRIS propane, PEG 3350

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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: Apr 19, 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
Reflection twinOperator: h,-k,-l / Fraction: 0.48
ReflectionResolution: 2.589→50 Å / Num. obs: 55871 / % possible obs: 94.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.027 / Rrim(I) all: 0.051 / Χ2: 0.96 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.643.60.36328710.930.2170.4240.77495.5
2.64-2.693.40.32227290.9320.210.3852.01594.6
2.69-2.743.40.24227990.9570.1510.2860.82894
2.74-2.83.20.15827050.9730.1020.1890.77491.7
2.8-2.863.40.1526820.9760.0940.1780.7892.1
2.86-2.933.70.13928580.9850.0830.1620.79297.4
2.93-33.80.11528850.9890.0680.1330.74696.9
3-3.083.70.09728600.9920.0570.1120.78497.1
3.08-3.173.70.07828560.9940.0460.090.78296.8
3.17-3.283.70.0728250.9950.0410.0810.8196.4
3.28-3.393.70.06128580.9950.0360.0710.82796.7
3.39-3.533.60.0727930.9870.0440.0831.34995.6
3.53-3.693.60.06327550.9880.040.0751.43894.2
3.69-3.883.50.04928300.9950.030.0581.23294.5
3.88-4.133.20.04725670.9890.0320.0571.34587.4
4.13-4.453.60.03428210.9980.020.0390.81196
4.45-4.893.80.03228250.9980.0190.0370.80996.8
4.89-5.63.80.03128280.9980.0180.0360.78795.5
5.6-7.053.70.03127410.9980.0190.0370.76893.4
7.05-503.60.02927830.9980.0180.0341.00394.3

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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: 2.6→48.956 Å / Cross valid method: THROUGHOUT / σ(F): 60.7 / Phase error: 29.58
RfactorNum. reflection% reflection
Rfree0.2613 2145 3.91 %
Rwork0.2301 --
obs0.2328 54848 92.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.17 Å2 / Biso mean: 45.2667 Å2 / Biso min: 16.75 Å2
Refinement stepCycle: final / Resolution: 2.6→48.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12722 0 0 322 13044
Biso mean---28.53 -
Num. residues----1612
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.65480.41861180.3372322075
2.6548-2.72660.37381130.3235346982
2.7266-2.80670.31551530.2735357985
2.8067-2.89730.37231420.2835390792
2.8973-3.00070.30631470.2687395794
3.0007-3.12080.28661600.257390693
3.1208-3.26260.26561510.2507391393
3.2626-3.43440.31051600.2518391993
3.4344-3.64930.23471360.2345382491
3.6493-3.93050.23331440.2377380590
3.9305-4.3250.23541540.2015372687
4.325-4.94850.22881400.1763391193
4.9485-6.22570.21361500.2044384591
6.2257-30.31970.22541520.1993381690
Refinement TLS params.Method: refined / Origin x: 19.4385 Å / Origin y: -0.2813 Å / Origin z: -0.1648 Å
111213212223313233
T0.2276 Å2-0.0348 Å2-0.0379 Å2-0.2603 Å2-0.0457 Å2--0.1675 Å2
L0.1731 °20.051 °2-0.266 °2-0.186 °2-0.3727 °2--0.457 °2
S-0.0102 Å °0.0289 Å °-0.0039 Å °0.0633 Å °0.0277 Å °-0.0015 Å °-0.0739 Å °-0.0387 Å °-0.0146 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 431
2X-RAY DIFFRACTION1allB6 - 431
3X-RAY DIFFRACTION1allC7 - 431
4X-RAY DIFFRACTION1allD8 - 431
5X-RAY DIFFRACTION1allS1 - 383

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