4Q9X | pdb_00004q9x

mTFP* PdCl2 soak

PDB DOI: https://doi.org/10.2210/pdb4Q9X/pdb

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

Deposited: 2014-05-02 Released: 2014-05-21
Deposition Author(s): Fischer, J., Quitterer, F., Groll, M., Eppinger, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.217 (Depositor), 0.222 (DCC)
R-Value Work:
0.176 (Depositor), 0.182 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

mTFP*: An imperishable and versatile protein host for anchoring diverse ligands and organocatalysts

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

To be published.

Macromolecule Content

Total Structure Weight: 26.28 kDa
Atom Count: 1,832
Modeled Residue Count: 214
Deposited Residue Count: 218
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GFP-like fluorescent chromoprotein cFP484	A	218	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PD Query on PD Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain O [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain O [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], O [auth A]	PALLADIUM ION Pd MUJIDPITZJWBSW-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth A]
CO3 Query on CO3 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], K [auth A], M [auth A], N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [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: 1.90 Å
R-Value Free: 0.217 (Depositor), 0.222 (DCC)
R-Value Work: 0.176 (Depositor), 0.182 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.47	α = 90
b = 83.63	β = 112.01
c = 37.82	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-05-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-05-21
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