3MVK | pdb_00003mvk

The Crystal Structure of FucU from Bifidobacterium longum to 1.65A

PDB DOI: https://doi.org/10.2210/pdb3MVK/pdb

Classification: ISOMERASE
Organism(s): Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-05-04 Released: 2010-05-12
Deposition Author(s): Stein, A.J., Xu, X., Cui, H., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.205 (Depositor), 0.205 (DCC)
R-Value Work:
0.182 (Depositor), 0.181 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The Crystal Structure of FucU from Bifidobacterium longum to 1.65A

Stein, A.J., Xu, X., Cui, H., Savchenko, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 164.02 kDa
Atom Count: 12,068
Modeled Residue Count: 1,408
Deposited Residue Count: 1,480
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein FucU	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	148	Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088	Mutation(s): 0 Gene Names: Blon_2305
UniProt
Find proteins for B7GNK7 (Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12)) Explore B7GNK7 Go to UniProtKB: B7GNK7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B7GNK7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain GA [auth G] SDF format, chain OA [auth J] SDF format, chain PA [auth J] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain Y [auth E] SDF format, chain Z [auth E] SDF format, chain Q [auth B] SDF format, chain M [auth A] SDF format, chain KA [auth H] SDF format, chain DA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain OA [auth J] MOL2 format, chain PA [auth J] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain M [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain DA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain OA [auth J] mmCIF format, chain PA [auth J] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain M [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain DA [auth F]	DA [auth F] GA [auth G] KA [auth H] M [auth A] OA [auth J] DA [auth F], GA [auth G], KA [auth H], M [auth A], OA [auth J], PA [auth J], Q [auth B], T [auth C], U [auth C], Y [auth E], Z [auth E]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Focus chain GA [auth G] Focus chain KA [auth H] Focus chain M [auth A] Focus chain OA [auth J] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain DA [auth F] Focus chain GA [auth G] Focus chain KA [auth H] Focus chain M [auth A] Focus chain OA [auth J] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth E] Focus chain Z [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain EA [auth F] SDF format, chain HA [auth G] SDF format, chain LA [auth H] SDF format, chain N [auth A] SDF format, chain R [auth B] MOL2 format, chain AA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] mmCIF format, chain AA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain R [auth B]	AA [auth E] EA [auth F] HA [auth G] LA [auth H] N [auth A] AA [auth E], EA [auth F], HA [auth G], LA [auth H], N [auth A], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain LA [auth H] Focus chain N [auth A] Focus chain R [auth B] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain LA [auth H] Focus chain N [auth A] Focus chain R [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain FA [auth G] SDF format, chain IA [auth H] SDF format, chain JA [auth H] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain MA [auth I] SDF format, chain NA [auth J] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain X [auth E] SDF format, chain W [auth E] SDF format, chain P [auth B] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth I] MOL2 format, chain NA [auth J] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] MOL2 format, chain W [auth E] MOL2 format, chain P [auth B] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain IA [auth H] mmCIF format, chain JA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth I] mmCIF format, chain NA [auth J] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain X [auth E] mmCIF format, chain W [auth E] mmCIF format, chain P [auth B]	BA [auth F] CA [auth F] FA [auth G] IA [auth H] JA [auth H] BA [auth F], CA [auth F], FA [auth G], IA [auth H], JA [auth H], K [auth A], L [auth A], MA [auth I], NA [auth J], O [auth B], P [auth B], S [auth C], V [auth D], W [auth E], X [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain CA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth I] Focus chain NA [auth J] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth E] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth I] Focus chain NA [auth J] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth E]

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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.205 (Depositor), 0.205 (DCC)
R-Value Work: 0.182 (Depositor), 0.181 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.047	α = 90
b = 83.859	β = 95.11
c = 144.813	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-05-12

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary