3RPL | pdb_00003rpl

D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase of Synechocystis sp. PCC 6803 in complex with FRUCTOSE-1,6-BISPHOSPHATE

PDB DOI: https://doi.org/10.2210/pdb3RPL/pdb

Classification: HYDROLASE
Organism(s): Synechocystis sp. PCC 6803
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-04-26 Released: 2012-05-02
Deposition Author(s): Hu, X., Hui, D., Lingling, F., Jian, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.207 (Depositor), 0.201 (DCC)
R-Value Work:
0.166 (Depositor), 0.161 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

New insights into the structural and interactional basis for a promising route towards fructose-1,6-/sedoheptulose-1,7-bisphosphatases controlling

Hu, X., Lingling, F.

To be published.

Macromolecule Content

Total Structure Weight: 166.98 kDa
Atom Count: 11,262
Modeled Residue Count: 1,389
Deposited Residue Count: 1,516
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase	A, C, D	379	Synechocystis sp. PCC 6803	Mutation(s): 0 Gene Names: slr2094 EC: 3.1.3.11 (PDB Primary Data), 3.1.3.37 (PDB Primary Data)
UniProt
Find proteins for P73922 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P73922 Go to UniProtKB: P73922
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P73922
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase	B	379	Synechocystis sp. PCC 6803	Mutation(s): 0 Gene Names: slr2094 EC: 3.1.3.11 (PDB Primary Data), 3.1.3.37 (PDB Primary Data)
UniProt
Find proteins for P73922 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P73922 Go to UniProtKB: P73922
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P73922
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain Z [auth C] SDF format, chain IA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain IA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain IA [auth D]	I [auth A], IA [auth D], N [auth B], Z [auth C]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain IA [auth D] Focus chain N [auth B] Focus chain Z [auth C] Interactions & Density Focus chain I [auth A] Focus chain IA [auth D] Focus chain N [auth B] Focus chain Z [auth C]
FBP Query on FBP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain MA [auth D] SDF format, chain R [auth B] SDF format, chain Y [auth C] MOL2 format, chain H [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain H [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain Y [auth C]	H [auth A], MA [auth D], R [auth B], Y [auth C]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain H [auth A] Focus chain MA [auth D] Focus chain R [auth B] Focus chain Y [auth C] Interactions & Density Focus chain H [auth A] Focus chain MA [auth D] Focus chain R [auth B] Focus chain Y [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain OA [auth D] SDF format, chain NA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain NA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain NA [auth D]	AA [auth C] BA [auth C] CA [auth C] J [auth A] K [auth A] AA [auth C], BA [auth C], CA [auth C], J [auth A], K [auth A], L [auth A], NA [auth D], OA [auth D], S [auth B], T [auth B], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain HA [auth C] MOL2 format, chain HA [auth C] mmCIF format, chain HA [auth C]	HA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Interactions & Density Focus chain HA [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain GA [auth C] SDF format, chain M [auth A] SDF format, chain PA [auth D] SDF format, chain FA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain FA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain FA [auth C]	DA [auth C] EA [auth C] FA [auth C] GA [auth C] M [auth A] DA [auth C], EA [auth C], FA [auth C], GA [auth C], M [auth A], PA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain M [auth A] Focus chain PA [auth D] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain M [auth A] Focus chain PA [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain LA [auth D] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain P [auth B] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain P [auth B] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain P [auth B] mmCIF format, chain G [auth A]	E [auth A] F [auth A] G [auth A] JA [auth D] KA [auth D] E [auth A], F [auth A], G [auth A], JA [auth D], KA [auth D], LA [auth D], O [auth B], P [auth B], Q [auth B], V [auth C], W [auth C], X [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	B	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.207 (Depositor), 0.201 (DCC)
R-Value Work: 0.166 (Depositor), 0.161 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.222	α = 90
b = 145.222	β = 90
c = 169.104	γ = 120

Software Package:

Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
PHENIX	refinement
CrysalisPro	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-05-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-05-02
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2023-12-06
Changes: Data collection
Version 1.4: 2024-10-30
Changes: Structure summary