2QE6 | pdb_00002qe6

CRYSTAL STRUCTURE OF A PUTATIVE METHYLTRANSFERASE (TFU_2867) FROM THERMOBIFIDA FUSCA YX AT 1.95 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb2QE6/pdb

Classification: TRANSFERASE
Organism(s): Thermobifida fusca YX
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-06-22 Released: 2007-07-03
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.213 (Depositor), 0.220 (DCC)
R-Value Work:
0.171 (Depositor), 0.180 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.7 of the entry. See complete history.

Literature

Crystal structure of uncharacterized protein Tfu_2867 (YP_290923.1) from Thermobifida fusca YX at 1.95 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 63.3 kDa
Atom Count: 4,528
Modeled Residue Count: 532
Deposited Residue Count: 548
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein Tfu_2867	A, B	274	Thermobifida fusca YX	Mutation(s): 1 Gene Names: YP_290923.1, Tfu_2867
UniProt
Find proteins for Q47KX2 (Thermobifida fusca (strain YX)) Explore Q47KX2 Go to UniProtKB: Q47KX2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q47KX2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A]	F [auth A], O [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain F [auth A] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain O [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] P [auth B] Q [auth B] G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B], R [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] J [auth B] K [auth B] C [auth A], D [auth A], E [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET
NEP Query on NEP	A, B	L-PEPTIDE LINKING	C₆ H₁₀ N₃ O₅ P		HIS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.213 (Depositor), 0.220 (DCC)
R-Value Work: 0.171 (Depositor), 0.180 (DCC)
R-Value Observed: 0.173 (Depositor)

Diffraction Data: https://doi.org/10.18430/M32QE6

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.627	α = 90
b = 76.024	β = 90
c = 81.315	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-07-03

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-07-03
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2017-10-25
Changes: Author supporting evidence
Version 1.5: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.6: 2021-10-20
Changes: Database references, Derived calculations
Version 1.7: 2023-01-25
Changes: Database references

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CRYSTAL STRUCTURE OF A PUTATIVE METHYLTRANSFERASE (TFU_2867) FROM THERMOBIFIDA FUSCA YX AT 1.95 A RESOLUTION

Crystal structure of uncharacterized protein Tfu_2867 (YP_290923.1) from Thermobifida fusca YX at 1.95 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations