4R6D | pdb_00004r6d

Modified mTFP* for enhanced metal binding: co-crystallization with CuCl2

PDB DOI: https://doi.org/10.2210/pdb4R6D/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Clavularia sp.
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-08-25 Released: 2014-11-12
Deposition Author(s): Fischer, J., Quitterer, F., Groll, M., Eppinger, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.194 (Depositor), 0.211 (DCC)
R-Value Work:
0.151 (Depositor), 0.165 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Modified mTFP* for enhanced metal binding: co-crystallization with CuCl2

Fischer, J., Quitterer, F., Groll, M., Eppinger, J.

To be published.

Macromolecule Content

Total Structure Weight: 24.95 kDa
Atom Count: 2,080
Modeled Residue Count: 214
Deposited Residue Count: 215
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GFP-like fluorescent chromoprotein cFP484	A	215	Clavularia sp.	Mutation(s): 32
UniProt
Find proteins for Q9U6Y3 (Clavularia sp.) Explore Q9U6Y3 Go to UniProtKB: Q9U6Y3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9U6Y3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PIA Query on PIA	A	L-PEPTIDE LINKING	C₁₄ H₁₅ N₃ O₄		ALA, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.194 (Depositor), 0.211 (DCC)
R-Value Work: 0.151 (Depositor), 0.165 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.198	α = 90
b = 67.656	β = 90
c = 84.271	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
PHASER	phasing
REFMAC	refinement
PROTEUM PLUS	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-11-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-12
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.