2VYX | pdb_00002vyx

Crystal structure of the T. thermophilus dodecin W38F mutant

PDB DOI: https://doi.org/10.2210/pdb2VYX/pdb

Classification: FLAVOPROTEIN
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2008-07-29 Released: 2009-11-17
Deposition Author(s): Essen, L.-O., Meissner, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.250 (Depositor), 0.219 (DCC)
R-Value Work:
0.218 (Depositor), 0.226 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Ultrafast Charge Transfer Dynamics in Flavoprotein Dodecin

Gurzadyan, G.G., Meissner, B., Sander, B., Essen, L.-O., Michel-Beyerle, M.E.

To be published.

Macromolecule Content

Total Structure Weight: 107.5 kDa
Atom Count: 7,888
Modeled Residue Count: 812
Deposited Residue Count: 828
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TTHA1431	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	69	Thermus thermophilus HB8	Mutation(s): 1
UniProt
Find proteins for Q5SIE3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIE3 Go to UniProtKB: Q5SIE3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SIE3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain S [auth B] SDF format, chain P [auth A] SDF format, chain OA [auth L] SDF format, chain NA [auth K] SDF format, chain N [auth A] SDF format, chain MA [auth J] SDF format, chain LA [auth I] SDF format, chain IA [auth G] SDF format, chain FA [auth F] SDF format, chain DA [auth E] SDF format, chain AA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain S [auth B] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth L] MOL2 format, chain NA [auth K] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth J] MOL2 format, chain LA [auth I] MOL2 format, chain IA [auth G] MOL2 format, chain FA [auth F] MOL2 format, chain DA [auth E] MOL2 format, chain AA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain S [auth B] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth L] mmCIF format, chain NA [auth K] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth J] mmCIF format, chain LA [auth I] mmCIF format, chain IA [auth G] mmCIF format, chain FA [auth F] mmCIF format, chain DA [auth E] mmCIF format, chain AA [auth D]	AA [auth D] DA [auth E] FA [auth F] IA [auth G] LA [auth I] AA [auth D], DA [auth E], FA [auth F], IA [auth G], LA [auth I], MA [auth J], N [auth A], NA [auth K], OA [auth L], P [auth A], S [auth B], W [auth C]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain AA [auth D] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain LA [auth I] Focus chain MA [auth J] Focus chain N [auth A] Focus chain NA [auth K] Focus chain OA [auth L] Focus chain P [auth A] Focus chain S [auth B] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain LA [auth I] Focus chain MA [auth J] Focus chain N [auth A] Focus chain NA [auth K] Focus chain OA [auth L] Focus chain P [auth A] Focus chain S [auth B] Focus chain W [auth C]
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain V [auth C] SDF format, chain Z [auth D] SDF format, chain X [auth C] SDF format, chain T [auth B] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain KA [auth H] SDF format, chain JA [auth H] SDF format, chain GA [auth F] SDF format, chain EA [auth F] SDF format, chain BA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain X [auth C] MOL2 format, chain T [auth B] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain GA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain BA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain X [auth C] mmCIF format, chain T [auth B] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain JA [auth H] mmCIF format, chain GA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain BA [auth D]	BA [auth D] EA [auth F] GA [auth F] JA [auth H] KA [auth H] BA [auth D], EA [auth F], GA [auth F], JA [auth H], KA [auth H], M [auth A], O [auth A], R [auth B], T [auth B], V [auth C], X [auth C], Z [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain BA [auth D] Focus chain EA [auth F] Focus chain GA [auth F] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain M [auth A] Focus chain O [auth A] Focus chain R [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth C] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth D] Focus chain EA [auth F] Focus chain GA [auth F] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain M [auth A] Focus chain O [auth A] Focus chain R [auth B] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth C] Focus chain Z [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain U [auth B] SDF format, chain Q [auth A] SDF format, chain CA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain U [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain CA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain U [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain CA [auth D]	CA [auth D], Q [auth A], U [auth B], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth D] Focus chain Q [auth A] Focus chain U [auth B] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth D] Focus chain Q [auth A] Focus chain U [auth B] Focus chain Y [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain HA [auth F] MOL2 format, chain HA [auth F] mmCIF format, chain HA [auth F]	HA [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain HA [auth F] Interactions & Density Focus chain HA [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.250 (Depositor), 0.219 (DCC)
R-Value Work: 0.218 (Depositor), 0.226 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.63	α = 90
b = 98.55	β = 90
c = 139.84	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-11-17

Deposition Author(s):

Essen, L.-O.

Meissner, B.

Revision History (Full details and data files)

Version 1.0: 2009-11-17
Type: Initial release
Version 1.1: 2011-05-07
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description