4RZ4 | pdb_00004rz4

Fructose-6-phosphate aldolase Q59E Y131F from E.coli

PDB DOI: https://doi.org/10.2210/pdb4RZ4/pdb

Classification: LYASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-12-18 Released: 2015-10-07
Deposition Author(s): Sandalova, T., Stellmacher, L., Leptihn, S., Schneider, G., Sprenger, G.A., Samland, A.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.196 (Depositor), 0.205 (DCC)
R-Value Work:
0.179 (Depositor), 0.189 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Acid Base Catalyst Discriminates between a Fructose 6-Phosphate Aldolase and a Transaldolase

Stellmacher, L., Sandalova, T., Leptihn, S., Schneider, G., Sprenger, G.A., Samland, A.K.

(2015) ChemCatChem

DOI: https://doi.org/10.1002/cctc.201500478

Macromolecule Content

Total Structure Weight: 242.61 kDa
Atom Count: 17,605
Modeled Residue Count: 2,200
Deposited Residue Count: 2,260
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-6-phosphate aldolase 1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	226	Escherichia coli K-12	Mutation(s): 2 Gene Names: b0825, fsa, fsaA, JW5109, mipB, ybiZ EC: 4.1.2
UniProt
Find proteins for P78055 (Escherichia coli (strain K12)) Explore P78055 Go to UniProtKB: P78055
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78055
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain EA [auth F] SDF format, chain MA [auth H] SDF format, chain NA [auth H] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain RA [auth I] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain UA [auth J] SDF format, chain VA [auth J] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain QA [auth I] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain JA [auth G] SDF format, chain IA [auth G] SDF format, chain FA [auth F] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain MA [auth H] MOL2 format, chain NA [auth H] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain RA [auth I] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain UA [auth J] MOL2 format, chain VA [auth J] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain QA [auth I] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth G] MOL2 format, chain IA [auth G] MOL2 format, chain FA [auth F] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain MA [auth H] mmCIF format, chain NA [auth H] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain RA [auth I] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain UA [auth J] mmCIF format, chain VA [auth J] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain QA [auth I] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth G] mmCIF format, chain IA [auth G] mmCIF format, chain FA [auth F]	AA [auth E] BA [auth E] EA [auth F] FA [auth F] IA [auth G] AA [auth E], BA [auth E], EA [auth F], FA [auth F], IA [auth G], JA [auth G], K [auth A], L [auth A], MA [auth H], NA [auth H], O [auth B], P [auth B], QA [auth I], RA [auth I], S [auth C], T [auth C], UA [auth J], VA [auth J], W [auth D], X [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain O [auth B] Focus chain P [auth B] Focus chain QA [auth I] Focus chain RA [auth I] Focus chain S [auth C] Focus chain T [auth C] Focus chain UA [auth J] Focus chain VA [auth J] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain JA [auth G] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain O [auth B] Focus chain P [auth B] Focus chain QA [auth I] Focus chain RA [auth I] Focus chain S [auth C] Focus chain T [auth C] Focus chain UA [auth J] Focus chain VA [auth J] Focus chain W [auth D] Focus chain X [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain SA [auth I] SDF format, chain WA [auth J] SDF format, chain Y [auth D] SDF format, chain U [auth C] SDF format, chain Q [auth B] SDF format, chain OA [auth H] SDF format, chain KA [auth G] SDF format, chain GA [auth F] SDF format, chain CA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain SA [auth I] MOL2 format, chain WA [auth J] MOL2 format, chain Y [auth D] MOL2 format, chain U [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain OA [auth H] MOL2 format, chain KA [auth G] MOL2 format, chain GA [auth F] MOL2 format, chain CA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain SA [auth I] mmCIF format, chain WA [auth J] mmCIF format, chain Y [auth D] mmCIF format, chain U [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain OA [auth H] mmCIF format, chain KA [auth G] mmCIF format, chain GA [auth F] mmCIF format, chain CA [auth E]	CA [auth E] GA [auth F] KA [auth G] M [auth A] OA [auth H] CA [auth E], GA [auth F], KA [auth G], M [auth A], OA [auth H], Q [auth B], SA [auth I], U [auth C], WA [auth J], Y [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth E] Focus chain GA [auth F] Focus chain KA [auth G] Focus chain M [auth A] Focus chain OA [auth H] Focus chain Q [auth B] Focus chain SA [auth I] Focus chain U [auth C] Focus chain WA [auth J] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain GA [auth F] Focus chain KA [auth G] Focus chain M [auth A] Focus chain OA [auth H] Focus chain Q [auth B] Focus chain SA [auth I] Focus chain U [auth C] Focus chain WA [auth J] Focus chain Y [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain N [auth A] SDF format, chain R [auth B] SDF format, chain TA [auth I] SDF format, chain V [auth C] SDF format, chain Z [auth D] SDF format, chain XA [auth J] SDF format, chain PA [auth H] SDF format, chain LA [auth G] SDF format, chain HA [auth F] MOL2 format, chain DA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth I] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain XA [auth J] MOL2 format, chain PA [auth H] MOL2 format, chain LA [auth G] MOL2 format, chain HA [auth F] mmCIF format, chain DA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain R [auth B] mmCIF format, chain TA [auth I] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain XA [auth J] mmCIF format, chain PA [auth H] mmCIF format, chain LA [auth G] mmCIF format, chain HA [auth F]	DA [auth E] HA [auth F] LA [auth G] N [auth A] PA [auth H] DA [auth E], HA [auth F], LA [auth G], N [auth A], PA [auth H], R [auth B], TA [auth I], V [auth C], XA [auth J], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth E] Focus chain HA [auth F] Focus chain LA [auth G] Focus chain N [auth A] Focus chain PA [auth H] Focus chain R [auth B] Focus chain TA [auth I] Focus chain V [auth C] Focus chain XA [auth J] Focus chain Z [auth D] Interactions & Density Focus chain DA [auth E] Focus chain HA [auth F] Focus chain LA [auth G] Focus chain N [auth A] Focus chain PA [auth H] Focus chain R [auth B] Focus chain TA [auth I] Focus chain V [auth C] Focus chain XA [auth J] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.196 (Depositor), 0.205 (DCC)
R-Value Work: 0.179 (Depositor), 0.189 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.44	α = 90
b = 133	β = 92.37
c = 102.27	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-10-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-10-07
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description