4MLZ

Crystal structure of periplasmic binding protein from Jonesia denitrificans

PDB DOI: https://doi.org/10.2210/pdb4MLZ/pdb

Classification: solute binding protein
Organism(s): Jonesia denitrificans DSM 20603
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-09-06 Released: 2013-09-18
Deposition Author(s): Chang, C., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.193
R-Value Work: 0.135
R-Value Observed: 0.138

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of periplasmic binding protein from Jonesia denitrificans

Chang, C., Chhor, G., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 70.51 kDa
Atom Count: 5,140
Modelled Residue Count: 598
Deposited Residue Count: 660
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein	A, B	330	Jonesia denitrificans DSM 20603	Mutation(s): 0 Gene Names: Jden_0967
UniProt
Find proteins for C7R301 (Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / BCRC 15368 / CIP 55.134 / JCM 11481 / NBRC 15587 / NCTC 10816 / Prevot 55134)) Explore C7R301 Go to UniProtKB: C7R301
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C7R301
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] H [auth B] C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	G [auth A], M [auth B], N [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.193
R-Value Work: 0.135
R-Value Observed: 0.138
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.678	α = 90
b = 72.741	β = 101.32
c = 71.306	γ = 90

Software Package:

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