3K13 | pdb_00003k13

Structure of the pterin-binding domain MeTr of 5-methyltetrahydrofolate-homocysteine methyltransferase from Bacteroides thetaiotaomicron

PDB DOI: https://doi.org/10.2210/pdb3K13/pdb

Classification: TRANSFERASE
Organism(s): Bacteroides thetaiotaomicron
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2009-09-25 Released: 2009-12-22
Deposition Author(s): Cuff, M.E., Li, H., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.188 (Depositor), 0.199 (DCC)
R-Value Work:
0.160 (Depositor), 0.174 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of the pterin-binding domain MeTr of 5-methyltetrahydrofolate-homocysteine methyltransferase from Bacteroides thetaiotaomicron

Cuff, M.E., Li, H., Cobb, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 103.46 kDa
Atom Count: 7,727
Modeled Residue Count: 859
Deposited Residue Count: 900
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-methyltetrahydrofolate-homocysteine methyltransferase	A, B, C	300	Bacteroides thetaiotaomicron	Mutation(s): 0 Gene Names: BT_0180 EC: 2.1.1.13
UniProt
Find proteins for Q8ABD0 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8ABD0 Go to UniProtKB: Q8ABD0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8ABD0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
THH Query on THH Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C] mmCIF format, chain E [auth A]	E [auth A], M [auth B], T [auth C]	N-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID C₂₀ H₂₅ N₇ O₆ ZNOVTXRBGFNYRX-STQMWFEESA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth C] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth C] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain V [auth C]	D [auth A] F [auth A] I [auth A] K [auth B] L [auth B] D [auth A], F [auth A], I [auth A], K [auth B], L [auth B], O [auth B], P [auth B], R [auth C], S [auth C], V [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth C]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain W [auth C] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain W [auth C] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C] mmCIF format, chain W [auth C]	J [auth A], N [auth B], Q [auth B], U [auth C], W [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain W [auth C] Interactions & Density Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain W [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: 2.00 Å
R-Value Free: 0.188 (Depositor), 0.199 (DCC)
R-Value Work: 0.160 (Depositor), 0.174 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.652	α = 90
b = 79.992	β = 90.12
c = 127.068	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-12-22

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-12-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary