3CNX | pdb_00003cnx

CRYSTAL STRUCTURE OF A PUTATIVE DEHYDRATASE FROM THE NTF2-LIKE FAMILY (SAV_4671) FROM STREPTOMYCES AVERMITILIS AT 2.10 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb3CNX/pdb

Classification: LYASE
Organism(s): Streptomyces avermitilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-03-26 Released: 2008-04-08
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.235 (Depositor), 0.240 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of NTF2-like protein of unknown function (NP_825848.1) from Streptomyces avermitilis at 2.10 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 56.38 kDa
Atom Count: 3,437
Modeled Residue Count: 432
Deposited Residue Count: 510
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	A, B, C	170	Streptomyces avermitilis	Mutation(s): 0 Gene Names: NP_825848.1, SAV4671
UniProt
Find proteins for Q82EE4 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)) Explore Q82EE4 Go to UniProtKB: Q82EE4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q82EE4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG6 Query on PG6 Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain T [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C]	G [auth A], H [auth A], O [auth B], T [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain T [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain T [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain S [auth C] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C]	M [auth B], N [auth B], S [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Interactions & Density Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain Q [auth C] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth C]	D [auth A], J [auth B], Q [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain Q [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain Q [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain P [auth C] MOL2 format, chain I [auth B] MOL2 format, chain P [auth C] mmCIF format, chain I [auth B] mmCIF format, chain P [auth C]	I [auth B], P [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain P [auth C] Interactions & Density Focus chain I [auth B] Focus chain P [auth C]
UNL Query on UNL Download Ideal Coordinates CCD File	E [auth A], K [auth B], R [auth C]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain R [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain R [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.235 (Depositor), 0.240 (DCC)
R-Value Work: 0.199 (Depositor), 0.200 (DCC)
R-Value Observed: 0.201 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33CNX

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103	α = 90
b = 128.75	β = 90
c = 44.38	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHARP	phasing
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-04-08

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-04-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-06
Changes: Data collection, Refinement description, Structure summary

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Help and Resources

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CRYSTAL STRUCTURE OF A PUTATIVE DEHYDRATASE FROM THE NTF2-LIKE FAMILY (SAV_4671) FROM STREPTOMYCES AVERMITILIS AT 2.10 A RESOLUTION

Crystal structure of NTF2-like protein of unknown function (NP_825848.1) from Streptomyces avermitilis at 2.10 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

3CNX | pdb_00003cnx