7NCC | pdb_00007ncc

Crystal structure of fructose-bisphosphate aldolase FBAP from Bacillus methanolicus

PDB DOI: https://doi.org/10.2210/pdb7NCC/pdb

Classification: LYASE
Organism(s): Bacillus methanolicus MGA3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-01-28 Released: 2021-02-17
Deposition Author(s): Einsle, O., Zhang, L., Guetle, D., Jacquot, J.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.252 (Depositor), 0.232 (DCC)
R-Value Work:
0.186 (Depositor)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Interrogating the Role of the Two Distinct Fructose-Bisphosphate Aldolases of Bacillus methanolicus by Site-Directed Mutagenesis of Key Amino Acids and Gene Repression by CRISPR Interference

Schultenkamper, K., Gutle, D.D., Lopez, M.G., Keller, L.B., Zhang, L., Einsle, O., Jacquot, J.P., Wendisch, V.F.

(2021) Front Microbiol 12: 933

DOI: https://doi.org/10.3389/fmicb.2021.669220

Macromolecule Content

Total Structure Weight: 61.79 kDa
Atom Count: 4,614
Modeled Residue Count: 568
Deposited Residue Count: 568
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative class II fructose-1,6-bisphosphate aldolase	A, B	284	Bacillus methanolicus MGA3	Mutation(s): 0 Gene Names: fba
UniProt
Find proteins for Q6TV43 (Bacillus methanolicus (strain MGA3 / ATCC 53907)) Explore Q6TV43 Go to UniProtKB: Q6TV43
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6TV43
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLT Query on MLT 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]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.252 (Depositor), 0.232 (DCC)
R-Value Work: 0.186 (Depositor)
R-Value Observed: 0.190 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.582	α = 90
b = 122.121	β = 90
c = 160.963	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-02-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-02-17
Type: Initial release
Version 1.1: 2021-05-26
Changes: Database references
Version 1.2: 2024-01-31
Changes: Data collection, Database references, Refinement description

7NCC | pdb_00007ncc

Crystal structure of fructose-bisphosphate aldolase FBAP from Bacillus methanolicus

Literature

Interrogating the Role of the Two Distinct Fructose-Bisphosphate Aldolases of Bacillus methanolicus by Site-Directed Mutagenesis of Key Amino Acids and Gene Repression by CRISPR Interference

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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