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- PDB-7c1h: Crystal structure of the starter condensation domain of rhizomide... -

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Basic information

Entry
Database: PDB / ID: 7c1h
TitleCrystal structure of the starter condensation domain of rhizomide synthetase RzmA
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-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: 2.3 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 4, 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)194,1764
Polymers194,1764
Non-polymers00
Water11,061614
1
A: Non-ribosomal peptide synthetase modules


Theoretical massNumber of molelcules
Total (without water)48,5441
Polymers48,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-ribosomal peptide synthetase modules


Theoretical massNumber of molelcules
Total (without water)48,5441
Polymers48,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non-ribosomal peptide synthetase modules


Theoretical massNumber of molelcules
Total (without water)48,5441
Polymers48,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Non-ribosomal peptide synthetase modules


Theoretical massNumber of molelcules
Total (without water)48,5441
Polymers48,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.051, 88.764, 97.883
Angle α, β, γ (deg.)67.300, 89.900, 89.920
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Non-ribosomal peptide synthetase modules


Mass: 48543.918 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: RzmA-Cs
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.: 614 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Description: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
Crystal growTemperature: 298 K / Method: vapor diffusion / 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: May 24, 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
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.296→50 Å / Num. obs: 78613 / % possible obs: 94.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.019 / Rrim(I) all: 0.036 / Χ2: 0.864 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.343.60.50539710.8680.3060.5910.87796.5
2.34-2.383.50.37540040.9260.2260.4380.88296.2
2.38-2.433.50.32438760.9390.1950.3790.90294.9
2.43-2.483.40.25638730.9580.1580.3020.90792.5
2.48-2.533.40.22537700.9650.1390.2650.91990.6
2.53-2.593.60.17840510.9810.1070.2080.93197.7
2.59-2.663.70.16440450.980.0980.1910.94197.6
2.66-2.733.60.13740960.9820.0820.161.05897
2.73-2.813.70.10339700.9910.0610.120.92196.6
2.81-2.93.60.08339910.9930.050.0970.93896.9
2.9-33.60.06540130.9950.0390.0760.91596.2
3-3.123.60.05238800.9960.0310.0610.89794.2
3.12-3.263.50.04336560.9960.0260.050.90688
3.26-3.443.70.03740140.9970.0220.0430.93596.9
3.44-3.653.70.03340650.9970.020.0390.95297.5
3.65-3.933.50.03238490.9970.020.0381.18992.7
3.93-4.333.70.02539110.9980.0150.0290.67494.2
4.33-4.953.50.02337340.9980.0140.0270.60289.5
4.95-6.243.80.02240230.9980.0130.0250.48797.2
6.24-503.70.0238210.9980.0120.0230.47391.9

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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: 4jn3

4jn3


Resolution: 2.3→49.974 Å / Cross valid method: THROUGHOUT / σ(F): 32.43 / Phase error: 27.9 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2525 2142 2.96 %
Rwork0.2273 70253 -
obs0.2297 72276 86.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.79 Å2 / Biso mean: 34.7831 Å2 / Biso min: 13.18 Å2
Refinement stepCycle: final / Resolution: 2.3→49.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12713 0 0 614 13327
Biso mean---28.75 -
Num. residues----1603
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.297-2.35440.3352950.28113059315452
2.3544-2.4180.34361050.27043686379162
2.418-2.48920.30521190.27264093421268
2.4892-2.56950.31911240.2624800492482
2.5695-2.66130.2961720.26495531570393
2.6613-2.76780.28691580.26245564572294
2.7678-2.89370.3151410.25895605574694
2.8937-3.04620.26751710.25185546571793
3.0462-3.2370.25581490.24735226537588
3.237-3.48670.26021520.23625522567493
3.4867-3.83720.21981580.21385598575694
3.8372-4.39160.23291430.19695315545890
4.3916-5.52960.19731590.18015343550289
5.5296-35.66130.23281520.21515365551791
Refinement TLS params.Method: refined / Origin x: 18.7006 Å / Origin y: 27.0609 Å / Origin z: -44.611 Å
111213212223313233
T0.1669 Å20.0068 Å2-0.0462 Å2-0.1856 Å2-0.04 Å2--0.1521 Å2
L0.1394 °20.0321 °2-0.1843 °2-0.1213 °2-0.2528 °2--0.3232 °2
S-0.0108 Å °0.028 Å °0.0027 Å °0.0267 Å °0.0321 Å °-0.0004 Å °-0.0289 Å °-0.044 Å °-0.0216 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 431
2X-RAY DIFFRACTION1allB7 - 431
3X-RAY DIFFRACTION1allC7 - 431
4X-RAY DIFFRACTION1allD7 - 431
5X-RAY DIFFRACTION1allS1 - 714

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