3BLZ | pdb_00003blz

Crystal structure of a ntf2-like protein of unknown function (sbal_0622) from shewanella baltica os155 at 1.75 A resolution

PDB DOI: https://doi.org/10.2210/pdb3BLZ/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Shewanella baltica OS155
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-12-11 Released: 2007-12-25
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.194 (Depositor), 0.200 (DCC)
R-Value Work:
0.152 (Depositor), 0.160 (DCC)
R-Value Observed:
0.154 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a NTF2-like protein of unknown function (YP_001049020.1) from Shewanella baltica OS155 at 1.75 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 170.7 kDa
Atom Count: 13,189
Modeled Residue Count: 1,483
Deposited Residue Count: 1,536
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NTF2-like protein of unknown function	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	128	Shewanella baltica OS155	Mutation(s): 0 Gene Names: YP_001049020.1, Sbal_0622
UniProt
Find proteins for A3D088 (Shewanella baltica (strain OS155 / ATCC BAA-1091)) Explore A3D088 Go to UniProtKB: A3D088
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3D088
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain EA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain EA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain EA [auth G]	EA [auth G], P [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth G] Focus chain P [auth B] Interactions & Density Focus chain EA [auth G] Focus chain P [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain Y [auth F] SDF format, chain X [auth F] SDF format, chain W [auth E] SDF format, chain V [auth E] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain PA [auth K] SDF format, chain OA [auth K] SDF format, chain O [auth B] SDF format, chain NA [auth K] SDF format, chain N [auth A] SDF format, chain MA [auth K] SDF format, chain M [auth A] SDF format, chain LA [auth J] SDF format, chain KA [auth J] SDF format, chain JA [auth I] SDF format, chain IA [auth I] SDF format, chain HA [auth I] SDF format, chain GA [auth H] SDF format, chain FA [auth H] SDF format, chain DA [auth G] SDF format, chain CA [auth G] SDF format, chain BA [auth F] SDF format, chain AA [auth F] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain X [auth F] MOL2 format, chain W [auth E] MOL2 format, chain V [auth E] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain PA [auth K] MOL2 format, chain OA [auth K] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth K] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth K] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth J] MOL2 format, chain KA [auth J] MOL2 format, chain JA [auth I] MOL2 format, chain IA [auth I] MOL2 format, chain HA [auth I] MOL2 format, chain GA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain X [auth F] mmCIF format, chain W [auth E] mmCIF format, chain V [auth E] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain PA [auth K] mmCIF format, chain OA [auth K] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth K] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth K] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth J] mmCIF format, chain KA [auth J] mmCIF format, chain JA [auth I] mmCIF format, chain IA [auth I] mmCIF format, chain HA [auth I] mmCIF format, chain GA [auth H] mmCIF format, chain FA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain CA [auth G] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth F] CA [auth G] DA [auth G] FA [auth H] AA [auth F], BA [auth F], CA [auth G], DA [auth G], FA [auth H], GA [auth H], HA [auth I], IA [auth I], JA [auth I], KA [auth J], LA [auth J], M [auth A], MA [auth K], N [auth A], NA [auth K], O [auth B], OA [auth K], PA [auth K], Q [auth C], R [auth C], S [auth C], T [auth D], U [auth D], V [auth E], W [auth E], X [auth F], Y [auth F], Z [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth I] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain KA [auth J] Focus chain LA [auth J] Focus chain M [auth A] Focus chain MA [auth K] Focus chain N [auth A] Focus chain NA [auth K] Focus chain O [auth B] Focus chain OA [auth K] Focus chain PA [auth K] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth I] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain KA [auth J] Focus chain LA [auth J] Focus chain M [auth A] Focus chain MA [auth K] Focus chain N [auth A] Focus chain NA [auth K] Focus chain O [auth B] Focus chain OA [auth K] Focus chain PA [auth K] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth F]

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, G, H, I, J, K, L	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: 0.194 (Depositor), 0.200 (DCC)
R-Value Work: 0.152 (Depositor), 0.160 (DCC)
R-Value Observed: 0.154 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33BLZ

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.085	α = 80.93
b = 58.121	β = 78.43
c = 140.462	γ = 60.6

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-12-25

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-12-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: 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: 2024-11-20
Changes: Data collection, Refinement description, Structure summary