3E8S | pdb_00003e8s

Crystal structure of Putative SAM Dependent Methyltransferase in Complex with SAH (NP_744700.1) from PSEUDOMONAS PUTIDA KT2440 at 2.10 A resolution

PDB DOI: https://doi.org/10.2210/pdb3E8S/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas putida KT2440
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-08-20 Released: 2008-09-02
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.176 (Depositor), 0.177 (DCC)
R-Value Work:
0.158 (Depositor), 0.161 (DCC)
R-Value Observed:
0.159 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of Putative SAM Dependent Methyltransferase in Complex with SAH (NP_744700.1) from PSEUDOMONAS PUTIDA KT2440 at 2.10 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 25.62 kDa
Atom Count: 2,000
Modeled Residue Count: 220
Deposited Residue Count: 227
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative SAM Dependent Methyltransferase	A	227	Pseudomonas putida KT2440	Mutation(s): 0 Gene Names: NP_744700.1, PP2555, PP_2555
UniProt
Find proteins for Q88JU2 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88JU2 Go to UniProtKB: Q88JU2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q88JU2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.176 (Depositor), 0.177 (DCC)
R-Value Work: 0.158 (Depositor), 0.161 (DCC)
R-Value Observed: 0.159 (Depositor)

Diffraction Data:

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.433	α = 90
b = 130.433	β = 90
c = 54.431	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
autoSHARP	phasing
SHELXD	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-09-02

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-09-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, 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: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.