7MJF

Crystal structure of Candidatus Liberibacter solanacearum dihydrodipicolinate synthase with pyruvate and succinic semi-aldehyde bound in active site

PDB DOI: https://doi.org/10.2210/pdb7MJF/pdb

Classification: LYASE
Organism(s): Candidatus Liberibacter solanacearum
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2021-04-20 Released: 2021-07-14
Deposition Author(s): Gilkes, J., Frampton, R.A., Board, A.J., Sheen, C.R., Smith, G.R., Dobson, R.C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.208
R-Value Work: 0.156
R-Value Observed: 0.158

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Candidatus Liberibacter solanacearum dihydrodipicolinate synthase with pyruvate and succinic semi-aldehyde bound in active site

Gilkes, J., Frampton, R.A., Board, A.J., Sheen, C.R., Smith, G.R., Dobson, R.C.J.

To be published.

Macromolecule Content

Total Structure Weight: 193.48 kDa
Atom Count: 14,512
Modelled Residue Count: 1,776
Deposited Residue Count: 1,776
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	A, B, C, D, E A, B, C, D, E, F	296	Candidatus Liberibacter solanacearum	Mutation(s): 0 Gene Names: dapA, DJ66_0589 EC: 4.3.3.7
UniProt
Find proteins for A0A0F4VK59 (Candidatus Liberibacter solanacearum) Explore A0A0F4VK59 Go to UniProtKB: A0A0F4VK59
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0F4VK59
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZGM Query on ZGM Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain Q [auth F] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], Q [auth F]	(4S)-4-hydroxy-2-oxoheptanedioic acid C₇ H₁₀ O₆ HNOAJOYERZTSNK-BYPYZUCNSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F]
E8U Query on E8U Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain R [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain R [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain R [auth F]	G [auth A] I [auth B] K [auth C] M [auth D] O [auth E] G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], R [auth F]	(4R)-4-oxidanyl-2-oxidanylidene-heptanedioic acid C₇ H₁₀ O₆ HNOAJOYERZTSNK-SCSAIBSYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.208
R-Value Work: 0.156
R-Value Observed: 0.158
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.101	α = 90
b = 132.881	β = 99.96
c = 155.062	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-07-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-07-14
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-03-13
Changes: Source and taxonomy
Version 1.3: 2024-10-30
Changes: Structure summary

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Help and Resources

7MJF

Crystal structure of Candidatus Liberibacter solanacearum dihydrodipicolinate synthase with pyruvate and succinic semi-aldehyde bound in active site

Crystal structure of Candidatus Liberibacter solanacearum dihydrodipicolinate synthase with pyruvate and succinic semi-aldehyde bound in active site

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)