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- EMDB-62988: PvdL-PCP2-E2-C3-A3 in complex with MLP (NRPS cross-module) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62988
TitlePvdL-PCP2-E2-C3-A3 in complex with MLP (NRPS cross-module)
Map data
Sample
  • Complex: PvdL-PCP2-E2-C3-A3 in complex with MLP (NRPS cross-module)
    • Protein or peptide: PvdL
    • Protein or peptide: MbtH-like domain-containing protein
KeywordsNonribosomal peptide synthetase / LIGASE
Function / homology
Function and homology information


monocarboxylic acid biosynthetic process / pyoverdine biosynthetic process / Actinobacterium-type cell wall biogenesis / siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / lipid biosynthetic process / ligase activity / catalytic activity / phosphopantetheine binding / antibiotic biosynthetic process ...monocarboxylic acid biosynthetic process / pyoverdine biosynthetic process / Actinobacterium-type cell wall biogenesis / siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / lipid biosynthetic process / ligase activity / catalytic activity / phosphopantetheine binding / antibiotic biosynthetic process / fatty acid metabolic process / cytosol
Similarity search - Function
MbtH-like protein / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain ...MbtH-like protein / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation 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
Similarity search - Domain/homology
PvdL / MbtH-like domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsWei C / Jialiang W / Zhijun W
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)2019YFA0905400 China
CitationJournal: To Be Published
Title: PvdL-PCP2-E2-C3-A3 in complex with MLP (NRPS cross-module)
Authors: Wei C / Jialiang W / Zhijun W
History
DepositionJan 5, 2025-
Header (metadata) releaseJan 7, 2026-
Map releaseJan 7, 2026-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62988.png

Downloads & links

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Map

FileDownload / File: emd_62988.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 340 pix.
= 280.16 Å		0.82 Å/pix.
x 340 pix.
= 280.16 Å		0.82 Å/pix.
x 340 pix.
= 280.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.2424984 - 0.4771606
Average (Standard dev.)-0.00014697535 (±0.011138062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 280.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62988_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62988_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PvdL-PCP2-E2-C3-A3 in complex with MLP (NRPS cross-module)

EntireName: PvdL-PCP2-E2-C3-A3 in complex with MLP (NRPS cross-module)
Components
  • Complex: PvdL-PCP2-E2-C3-A3 in complex with MLP (NRPS cross-module)
    • Protein or peptide: PvdL
    • Protein or peptide: MbtH-like domain-containing protein

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Supramolecule #1: PvdL-PCP2-E2-C3-A3 in complex with MLP (NRPS cross-module)

SupramoleculeName: PvdL-PCP2-E2-C3-A3 in complex with MLP (NRPS cross-module)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 193 kDa/nm

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Macromolecule #1: PvdL

MacromoleculeName: PvdL / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 185.452781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGAPRSVLE QQLAGVWREV LNVERVGLGD NFFELGGD(4HH)I LSIQVVSRAR QLGIHFSPRD LFQHQT VQS LAAVARHSQA SQAEQGPVQG DSALTPIQHW FFDLPLARRE HWNQALLLQP RQAIDLGLLR KSLQRLVEQH DALRLAF RQ VDGEWLAQHR ...String:
MGSSHHHHHH SSGAPRSVLE QQLAGVWREV LNVERVGLGD NFFELGGD(4HH)I LSIQVVSRAR QLGIHFSPRD LFQHQT VQS LAAVARHSQA SQAEQGPVQG DSALTPIQHW FFDLPLARRE HWNQALLLQP RQAIDLGLLR KSLQRLVEQH DALRLAF RQ VDGEWLAQHR PLREQELLWH VPVQSFDECA ELFAKAQRSL DLEQGPLLRA VLVDGPAGEQ RLLLAIHHLV VDGVSWRV L LEDLQQVYRQ FAEGAEPALP AKTSAFRDWA GRLQAYAGSE SLREELGWWQ ARLGGQPVEW PCDRPQGDNR EALAESVSL RLDPQRTRQL LQQAPAAYRT QVNDLLLTAL ARVLCRWSGQ PSTLVQLEGH GREALFDDID LTRSVGWFTS AYPLRLTPAQ SPGESIKAI KEQLRAVPHK GLGYGVLRYL ADPAVRQAMA ALPTAPITFN YLGQFDQSFA DALFQPLDQP TGPIHDEQAP L PNELSVDG QVYGGELVLR WTYSRERYDA RTVNELAQAY LAELQALIEH CLEDGAGGLT PSDFPLAQLS QAQLDALAVP AG EIEDVYP LTPMQEGLLL HTLLEPGTGI YYMQDRYRID SPLDPERFAA AWQAVVARHE ALRASFVWNA GETMLQVIHK PGR TRIEFL DWSELPEDGH EERLQALHKR EREAGFDLLE QPPFHLRLIR LGEARYWFMM SNHHILIDAW CRGLLMNDFF EIYS ALGES RPANLPTPPR YRDYIAWLQR QDLEQSRRWW SESLRGFERP TLVPSDRPFL REHAGESGGM IVGDRYTRLD AADGA RLRE LAQRYQLTVN TFAQAAWALT LRRFSGERDV LFGVTVAGRP VGMPEMQRTV GLFINSIPLR VQMPAAGQRC TVREWL NRL FERNLELREH EHLPLVAIQE SSELPKGQPL FDSLFVFENA PVEVSVLDRA QSLNASSDSG RTHTNFPLTV VCYPGDD LG LHLSYDQRYF EAPTVERLLG EFKRLLLALA DGFHGELEAL PLLGEDERDF LLDGCNRSAR DYPLEQGYVR LFEAQVAA H PQRIAASCLE QRWSYAELNR RANRLGHALR AAGVGIDQPV ALLAERGLDL LGMIVGSFKA GAGYLPLDPG HPTQRLTRI VELSRTLVLV CTQACREQAL ALFDELGCVD RPRLLVWDEI QQGEGAEHDP QVYSGPQNLA YVIYTSGSTG LPKGVMVEQA GMLNNQLSK VPYLELDEND VIAQTASQSF DISVWQFLAA PLFGARVAIV PNAVAHDPQG LLAHVGEQGI TVLESVPSLI Q GMLAEERQ ALDGLRWMLP TGEAMPPELA RQWLKRYPRI GLVNAYGPAE CSDDVAFFRV DLASTESTYL PIGSPTDNNR LY LLGAGAD DAFELVPLGA VGELCVAGTG VGRGYVGDPL RTAQAFVPHP FGAPGERLYR TGDLARRRAD GVLEYVGRID HQV KIRGFR IELGEIEARL HERADVREAA VAVQEGANGK YLVGYLVPGE TPRSSADSPA GLMVEQGAWF ERIKQQLRAD LPDY MVPLH WLVLDRMPLN ANGKLDRKAL PALDIGQMQN QAYQAPRNEL EETLARIWAE VLKVERVGVF DNFFELGGHS LLATQ IASR VQKALQRNVP LRAMFECTTV EELASYIESL APSEISEQKA ERLNDLMSKL EML

UniProtKB: PvdL

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Macromolecule #2: MbtH-like domain-containing protein

MacromoleculeName: MbtH-like domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 9.856021 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTSVFDRDDI QFQVVVNHEE QYSIWPEYKE IPQGWRAAGK SGLKKDCLAY IEEVWTDMRP LSLRQHMDKA AGSTGNWSHP QFEK

UniProtKB: MbtH-like domain-containing protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 39806
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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