3LVU | pdb_00003lvu

Crystal structure of ABC transporter, periplasmic substrate-binding protein SPO2066 from Silicibacter pomeroyi

PDB DOI: https://doi.org/10.2210/pdb3LVU/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Ruegeria pomeroyi
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-02-22 Released: 2010-03-02
Deposition Author(s): Chang, C., Chhor, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.205 (Depositor), 0.215 (DCC)
R-Value Work:
0.169 (Depositor), 0.182 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of ABC transporter, periplasmic substrate-binding protein SPO2066 from Silicibacter pomeroyi

Chang, C., Chhor, G., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 117.26 kDa
Atom Count: 9,093
Modeled Residue Count: 1,031
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, periplasmic substrate-binding protein	A, B, C, D	258	Ruegeria pomeroyi	Mutation(s): 0 Gene Names: SPO2066
UniProt
Find proteins for Q5LRQ9 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LRQ9 Go to UniProtKB: Q5LRQ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5LRQ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG5 Query on PG5 Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B]	P [auth B], Q [auth B]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C₈ H₁₈ O₄ YFNKIDBQEZZDLK-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain P [auth B] Focus chain Q [auth B]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] E [auth A] F [auth A] G [auth A] AA [auth D], BA [auth D], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B], T [auth C], U [auth C], V [auth C], Y [auth D], Z [auth D]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain O [auth B] SDF format, chain H [auth A] MOL2 format, chain W [auth C] MOL2 format, chain O [auth B] MOL2 format, chain H [auth A] mmCIF format, chain W [auth C] mmCIF format, chain O [auth B] mmCIF format, chain H [auth A]	H [auth A], O [auth B], W [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth B] Focus chain W [auth C] Interactions & Density Focus chain H [auth A] Focus chain O [auth B] Focus chain W [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] MOL2 format, chain X [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] mmCIF format, chain X [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B]	M [auth B], N [auth B], R [auth B], S [auth B], X [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Interactions & Density Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.205 (Depositor), 0.215 (DCC)
R-Value Work: 0.169 (Depositor), 0.182 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.384	α = 82.63
b = 75.517	β = 80.29
c = 78.477	γ = 77.42

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-02

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-03-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary