3B8L | pdb_00003b8l

CRYSTAL STRUCTURE OF A PUTATIVE AROMATIC RING HYDROXYLASE (SARO_3538) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM AT 1.75 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb3B8L/pdb

Classification: OXIDOREDUCTASE
Organism(s): Novosphingobium aromaticivorans DSM 12444
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-01 Released: 2007-11-27
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.199 (Depositor), 0.202 (DCC)
R-Value Work:
0.167 (Depositor), 0.172 (DCC)
R-Value Observed:
0.169 (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 (YP_001165924.1) from Novosphingobium aromaticivorans DSM 12444 at 1.75 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 113 kDa
Atom Count: 7,917
Modeled Residue Count: 866
Deposited Residue Count: 978
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D, E A, B, C, D, E, F	163	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0 Gene Names: YP_001165924.1, Saro_3538
UniProt
Find proteins for A4XEN7 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore A4XEN7 Go to UniProtKB: A4XEN7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4XEN7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain S [auth F] SDF format, chain R [auth F] SDF format, chain Q [auth E] SDF format, chain P [auth E] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain S [auth F] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth E] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain S [auth F] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth E] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth B] K [auth C] L [auth C] G [auth A], H [auth A], I [auth B], K [auth C], L [auth C], N [auth D], O [auth D], P [auth E], Q [auth E], R [auth F], S [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.199 (Depositor), 0.202 (DCC)
R-Value Work: 0.167 (Depositor), 0.172 (DCC)
R-Value Observed: 0.169 (Depositor)

Diffraction Data:

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.85	α = 90
b = 95.85	β = 90
c = 232.3	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-11-27

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-11-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, 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: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-10-16
Changes: Data collection, Structure summary

3B8L | pdb_00003b8l

CRYSTAL STRUCTURE OF A PUTATIVE AROMATIC RING HYDROXYLASE (SARO_3538) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM AT 1.75 A RESOLUTION

Literature

Crystal structure of NTF2-like protein of unknown function (YP_001165924.1) from Novosphingobium aromaticivorans DSM 12444 at 1.75 A resolution

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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