2RAQ | pdb_00002raq

Crystal structure of the MTH889 protein from Methanothermobacter thermautotrophicus. Northeast Structural Genomics Consortium target TT205

PDB DOI: https://doi.org/10.2210/pdb2RAQ/pdb

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

Deposited: 2007-09-17 Released: 2007-10-16
Deposition Author(s): Forouhar, F., Su, M., Xu, X., Seetharaman, J., Mao, L., Xiao, R., Ma, L.-C., Conover, K., Baran, M.C., Acton, T.B., Montelione, G.T., Arrowsmith, C.H., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free:
0.280 (Depositor), 0.279 (DCC)
R-Value Work:
0.216 (Depositor), 0.216 (DCC)
R-Value Observed:
0.219 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the MTH889 protein from Methanothermobacter thermautotrophicus.

Forouhar, F., Su, M., Xu, X., Seetharaman, J., Mao, L., Xiao, R., Ma, L.-C., Conover, K., Baran, M.C., Acton, T.B., Montelione, G.T., Arrowsmith, C.H., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 77.3 kDa
Atom Count: 5,150
Modeled Residue Count: 652
Deposited Residue Count: 679
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved protein MTH889	A, B, C, D, E A, B, C, D, E, F, G	97	Methanothermobacter thermautotrophicus str. Delta H	Mutation(s): 0 Gene Names: MTH889
UniProt
Find proteins for O26975 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26975 Go to UniProtKB: O26975
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O26975
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain U [auth G] SDF format, chain T [auth F] SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain Q [auth E] SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain U [auth G] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain U [auth G] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth B] H [auth A], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth E], S [auth E], T [auth F], U [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G]

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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free: 0.280 (Depositor), 0.279 (DCC)
R-Value Work: 0.216 (Depositor), 0.216 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.569	α = 90
b = 113.569	β = 90
c = 114.53	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
RESOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-10-16

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-10-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Database references, Structure summary
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary