1RPJ

CRYSTAL STRUCTURE OF D-ALLOSE BINDING PROTEIN FROM ESCHERICHIA COLI

PDB DOI: https://doi.org/10.2210/pdb1RPJ/pdb

Classification: PERIPLASMIC SUGAR RECEPTOR
Organism(s): Escherichia coli K-12
Mutation(s): No

Deposited: 1999-02-04 Released: 1999-02-16
Deposition Author(s): Chaudhuri, B., Jones, T.A., Mowbray, S.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.245
R-Value Work: 0.194

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 30.76 kDa
Atom Count: 2,366
Modelled Residue Count: 288
Deposited Residue Count: 288
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PRECURSOR OF PERIPLASMIC SUGAR RECEPTOR)	A	288	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P39265 (Escherichia coli (strain K12)) Explore P39265 Go to UniProtKB: P39265
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P39265
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ALL Query on ALL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	beta-D-allopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-QZABAPFNSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
ALL	PDBBind: 1RPJ	Kd: 330 (nM) from 1 assay(s)
ALL	Binding MOAD: 1RPJ	Kd: 330 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.245
R-Value Work: 0.194
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.38	α = 90
b = 67.82	β = 96.71
c = 53.59	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1999-02-16

Deposition Author(s):

Chaudhuri, B.

Jones, T.A.

Mowbray, S.L.

Revision History (Full details and data files)

Version 1.0: 1999-02-16
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2017-11-15
Changes: Atomic model
Version 2.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 2.2: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary

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1RPJ

CRYSTAL STRUCTURE OF D-ALLOSE BINDING PROTEIN FROM ESCHERICHIA COLI

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)