6LRP | pdb_00006lrp

Crystal structure of isocitrate lyase (Caur_3889) from Chloroflexus aurantiacus in complex with manganese ion

PDB DOI: https://doi.org/10.2210/pdb6LRP/pdb

Classification: LYASE
Organism(s): Chloroflexus aurantiacus J-10-fl
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-01-16 Released: 2021-07-28
Deposition Author(s): Lee, S.H., Kim, K.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.223 (Depositor), 0.232 (DCC)
R-Value Work:
0.175 (Depositor), 0.185 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structural studies reveal the molecular mechanism of isocitrate lyase from Chloroflexus aurantiacus

Lee, S.H., Kim, K.J.

To be published.

Macromolecule Content

Total Structure Weight: 48.63 kDa
Atom Count: 3,302
Modeled Residue Count: 390
Deposited Residue Count: 436
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate lyase	A	436	Chloroflexus aurantiacus J-10-fl	Mutation(s): 0 Gene Names: Caur_3889 EC: 4.1.3.1
UniProt
Find proteins for A9WDE7 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)) Explore A9WDE7 Go to UniProtKB: A9WDE7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9WDE7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P3G Query on P3G Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	3,6,9,12,15-PENTAOXAHEPTADECANE C₁₂ H₂₆ O₅ HYDWALOBQJFOMS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.223 (Depositor), 0.232 (DCC)
R-Value Work: 0.175 (Depositor), 0.185 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.772	α = 90
b = 92.772	β = 90
c = 216.114	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-07-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-07-28
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.