3T5T | pdb_00003t5t

Vall from streptomyces hygroscopicus in apo form

PDB DOI: https://doi.org/10.2210/pdb3T5T/pdb

Classification: TRANSFERASE
Organism(s): Streptomyces hygroscopicus subsp. limoneus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-07-28 Released: 2012-08-01
Deposition Author(s): Zhang, H., Zheng, L., Qian, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.209 (Depositor), 0.224 (DCC)
R-Value Work:
0.179 (Depositor), 0.198 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural basis for the substrate specificity of ValL

Zhang, H., Zheng, L., Qian, H.

To be published.

Macromolecule Content

Total Structure Weight: 110.08 kDa
Atom Count: 8,233
Modeled Residue Count: 945
Deposited Residue Count: 992
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glycosyltransferase	A, B	496	Streptomyces hygroscopicus subsp. limoneus	Mutation(s): 0 Gene Names: vldE EC: 2.5.1.135
UniProt
Find proteins for Q15JG1 (Streptomyces hygroscopicus subsp. limoneus) Explore Q15JG1 Go to UniProtKB: Q15JG1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15JG1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	H [auth A], L [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions 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 I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density 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 I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.209 (Depositor), 0.224 (DCC)
R-Value Work: 0.179 (Depositor), 0.198 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.671	α = 90
b = 46.693	β = 108.08
c = 123.879	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-08-01

Deposition Author(s):

Zhang, H.

Zheng, L.

Qian, H.

Revision History (Full details and data files)

Version 1.0: 2012-08-01
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

3T5T | pdb_00003t5t

Vall from streptomyces hygroscopicus in apo form

Literature

Structural basis for the substrate specificity of ValL

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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