2PTF | pdb_00002ptf

Crystal structure of protein MTH_863 from Methanobacterium thermoautotrophicum bound to FMN

PDB DOI: https://doi.org/10.2210/pdb2PTF/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Methanothermobacter thermautotrophicus str. Delta H
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-05-08 Released: 2007-05-15
Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Iizuka, M., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.253 (Depositor), 0.236 (DCC)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.7 of the entry. See complete history.

Literature

Crystal structure of protein MTH_863 from Methanobacterium thermoautotrophicum bound to FMN.

Bonanno, J.B., Rutter, M., Bain, K.T., Iizuka, M., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 53.76 kDa
Atom Count: 3,382
Modeled Residue Count: 400
Deposited Residue Count: 466
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein MTH_863	A, B	233	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0 Gene Names: MTH_863
UniProt
Find proteins for O26951 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26951 Go to UniProtKB: O26951
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O26951
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.253 (Depositor), 0.236 (DCC)
R-Value Work: 0.199 (Depositor)
R-Value Observed: 0.201 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.727	α = 90
b = 91.727	β = 90
c = 117.868	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
DENZO	data reduction
CCP4	data scaling
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-05-15

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-05-15
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2012-10-24
Changes: Structure summary
Version 1.4: 2017-10-18
Changes: Refinement description
Version 1.5: 2018-11-14
Changes: Data collection, Structure summary
Version 1.6: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.7: 2024-02-21
Changes: Data collection, Database references