3OM4 | pdb_00003om4

Crystal structure of B. megaterium levansucrase mutant K373A

PDB DOI: https://doi.org/10.2210/pdb3OM4/pdb

Classification: TRANSFERASE
Organism(s): Priestia megaterium
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-08-26 Released: 2011-03-23
Deposition Author(s): Strube, C.P., Homann, A., Gamer, M., Jahn, D., Seibel, J., Heinz, D.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.213 (Depositor), 0.213 (DCC)
R-Value Work:
0.202 (Depositor), 0.201 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of B. megaterium levansucrase mutant K373A

Strube, C.P., Homann, A., Gamer, M., Jahn, D., Seibel, J., Heinz, D.W.

To be published.

Macromolecule Content

Total Structure Weight: 205.85 kDa
Atom Count: 15,821
Modeled Residue Count: 1,792
Deposited Residue Count: 1,824
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Levansucrase	A, B, C, D	456	Priestia megaterium	Mutation(s): 1 Gene Names: sacB EC: 2.4.1.10
UniProt
Find proteins for D5DC07 (Priestia megaterium (strain DSM 319 / IMG 1521)) Explore D5DC07 Go to UniProtKB: D5DC07
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D5DC07
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain S [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain S [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], K [auth B], O [auth C], S [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D]
PEG Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A] L [auth B] P [auth C] Q [auth C] T [auth D] H [auth A], L [auth B], P [auth C], Q [auth C], T [auth D], U [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain M [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain R [auth D] MOL2 format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain R [auth D] mmCIF format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], M [auth C], R [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.213 (Depositor), 0.213 (DCC)
R-Value Work: 0.202 (Depositor), 0.201 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.585	α = 90
b = 100.075	β = 90.67
c = 95.544	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-03-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-03-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations