6F73

Crystal structure of VAO-type flavoprotein MtVAO615 at pH 5.0 from Myceliophthora thermophila C1

PDB DOI: https://doi.org/10.2210/pdb6F73/pdb

Classification: FLAVOPROTEIN
Organism(s): Thermothelomyces thermophilus ATCC 42464
Expression System: Thermothelomyces thermophilus ATCC 42464
Mutation(s): No

Deposited: 2017-12-07 Released: 2018-01-10
Deposition Author(s): Rozeboom, H.J., Fraaije, M.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.235
R-Value Work: 0.193
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 128.02 kDa
Atom Count: 9,468
Modelled Residue Count: 1,096
Deposited Residue Count: 1,148
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MtVAO615	A, B	574	Thermothelomyces thermophilus ATCC 42464	Mutation(s): 0 Gene Names: MYCTH_2305637
UniProt
Find proteins for G2QDQ9 (Thermothelomyces thermophilus (strain ATCC 42464 / BCRC 31852 / DSM 1799)) Explore G2QDQ9 Go to UniProtKB: G2QDQ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G2QDQ9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B]	F [auth A] G [auth A] I [auth B] J [auth B] K [auth B] F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.235
R-Value Work: 0.193
R-Value Observed: 0.195
Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.417	α = 90
b = 115.959	β = 90
c = 198.676	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-01-10

Deposition Author(s):

Rozeboom, H.J.

Fraaije, M.W.

Revision History (Full details and data files)

Version 1.0: 2018-01-10
Type: Initial release
Version 1.1: 2018-01-17
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

6F73

Crystal structure of VAO-type flavoprotein MtVAO615 at pH 5.0 from Myceliophthora thermophila C1

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)