2CGL

Crystal Structure of L-rhamnulose kinase from Escherichia coli in complex with L-fructose, ADP and a modeled ATP gamma phosphate.

PDB DOI: https://doi.org/10.2210/pdb2CGL/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli BL21(DE3)
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-03-09 Released: 2006-05-31
Deposition Author(s): Grueninger, D., Schulz, G.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.209
R-Value Work: 0.167
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 55.11 kDa
Atom Count: 3,958
Modelled Residue Count: 479
Deposited Residue Count: 489
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RHAMNULOKINASE	A	489	Escherichia coli BL21(DE3)	Mutation(s): 3 EC: 2.7.1.5
UniProt
Find proteins for P32171 (Escherichia coli (strain K12)) Explore P32171 Go to UniProtKB: P32171
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32171
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
LFR Query on LFR Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	beta-L-fructofuranose C₆ H₁₂ O₆ RFSUNEUAIZKAJO-AZGQCCRYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO3 Query on PO3 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	PHOSPHITE ION O₃ P AQSJGOWTSHOLKH-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.209
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.781	α = 90
b = 50.966	β = 90
c = 158.102	γ = 90

Software Package:

Software Name	Purpose
autoSHARP	model building
XSCALE	data scaling
SHELXD	phasing
SHELXE	phasing
SHARP	phasing
autoSHARP	phasing
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-05-31

Deposition Author(s):

Grueninger, D.

Schulz, G.E.

Revision History (Full details and data files)

Version 1.0: 2006-05-31
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2018-10-24
Changes: Advisory, Data collection, Source and taxonomy
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary

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Help and Resources

2CGL

Crystal Structure of L-rhamnulose kinase from Escherichia coli in complex with L-fructose, ADP and a modeled ATP gamma phosphate.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)