5DS0 | pdb_00005ds0

Crystal structure of TET aminopeptidase from marine sediment archaeon Thaumarchaeota archaeon SCGC AB-539-E09

PDB DOI: https://doi.org/10.2210/pdb5DS0/pdb

Classification: HYDROLASE
Organism(s): Thaumarchaeota archaeon SCGC AB-539-E09
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-09-16 Released: 2015-10-14
Deposition Author(s): Michalska, K., Chhor, G., Mootz, J., Endres, M., Jedrzejczak, R., Babnigg, G., Steen, A., Lloyd, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.206 (Depositor), 0.202 (DCC)
R-Value Work:
0.193 (Depositor), 0.194 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of TET aminopeptidase from marine sediment archaeon Thaumarchaeota archaeon SCGC AB-539-E09

Michalska, K., Chhor, G., Mootz, J., Endres, M., Jedrzejczak, R., Babnigg, G., Steen, A., Lloyd, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 480.81 kDa
Atom Count: 32,797
Modeled Residue Count: 4,276
Deposited Residue Count: 4,308
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase M42	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	359	Thaumarchaeota archaeon SCGC AB-539-E09	Mutation(s): 0 Gene Names: MCGE09_00274
UniProt
Find proteins for A0ACD6B9R9 (Thaumarchaeota archaeon SCGC AB-539-E09) Explore A0ACD6B9R9 Go to UniProtKB: A0ACD6B9R9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9R9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain YA [auth L] SDF format, chain W [auth C] SDF format, chain VA [auth K] SDF format, chain V [auth C] SDF format, chain SA [auth J] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain PA [auth I] SDF format, chain OA [auth I] SDF format, chain O [auth A] SDF format, chain LA [auth H] SDF format, chain KA [auth H] SDF format, chain HA [auth G] SDF format, chain GA [auth G] SDF format, chain BA [auth E] MOL2 format, chain YA [auth L] MOL2 format, chain W [auth C] MOL2 format, chain VA [auth K] MOL2 format, chain V [auth C] MOL2 format, chain SA [auth J] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain PA [auth I] MOL2 format, chain OA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain KA [auth H] MOL2 format, chain HA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain BA [auth E] mmCIF format, chain YA [auth L] mmCIF format, chain W [auth C] mmCIF format, chain VA [auth K] mmCIF format, chain V [auth C] mmCIF format, chain SA [auth J] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain PA [auth I] mmCIF format, chain OA [auth I] mmCIF format, chain O [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain KA [auth H] mmCIF format, chain HA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain BA [auth E]	BA [auth E] GA [auth G] HA [auth G] KA [auth H] LA [auth H] BA [auth E], GA [auth G], HA [auth G], KA [auth H], LA [auth H], O [auth A], OA [auth I], PA [auth I], R [auth B], S [auth B], SA [auth J], V [auth C], VA [auth K], W [auth C], YA [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain O [auth A] Focus chain OA [auth I] Focus chain PA [auth I] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth J] Focus chain V [auth C] Focus chain VA [auth K] Focus chain W [auth C] Focus chain YA [auth L] Interactions & Density Focus chain BA [auth E] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain O [auth A] Focus chain OA [auth I] Focus chain PA [auth I] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth J] Focus chain V [auth C] Focus chain VA [auth K] Focus chain W [auth C] Focus chain YA [auth L]
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain Y [auth D] SDF format, chain XA [auth L] SDF format, chain X [auth D] SDF format, chain WA [auth L] SDF format, chain UA [auth K] SDF format, chain U [auth C] SDF format, chain TA [auth K] SDF format, chain T [auth C] SDF format, chain RA [auth J] SDF format, chain QA [auth J] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain NA [auth I] SDF format, chain N [auth A] SDF format, chain MA [auth I] SDF format, chain M [auth A] SDF format, chain JA [auth H] SDF format, chain IA [auth H] SDF format, chain FA [auth G] SDF format, chain EA [auth G] SDF format, chain DA [auth F] SDF format, chain CA [auth F] SDF format, chain AA [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain XA [auth L] MOL2 format, chain X [auth D] MOL2 format, chain WA [auth L] MOL2 format, chain UA [auth K] MOL2 format, chain U [auth C] MOL2 format, chain TA [auth K] MOL2 format, chain T [auth C] MOL2 format, chain RA [auth J] MOL2 format, chain QA [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain NA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain IA [auth H] MOL2 format, chain FA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain XA [auth L] mmCIF format, chain X [auth D] mmCIF format, chain WA [auth L] mmCIF format, chain UA [auth K] mmCIF format, chain U [auth C] mmCIF format, chain TA [auth K] mmCIF format, chain T [auth C] mmCIF format, chain RA [auth J] mmCIF format, chain QA [auth J] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain NA [auth I] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain IA [auth H] mmCIF format, chain FA [auth G] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] CA [auth F] DA [auth F] EA [auth G] FA [auth G] AA [auth E], CA [auth F], DA [auth F], EA [auth G], FA [auth G], IA [auth H], JA [auth H], M [auth A], MA [auth I], N [auth A], NA [auth I], P [auth B], Q [auth B], QA [auth J], RA [auth J], T [auth C], TA [auth K], U [auth C], UA [auth K], WA [auth L], X [auth D], XA [auth L], Y [auth D], Z [auth E]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain NA [auth I] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain T [auth C] Focus chain TA [auth K] Focus chain U [auth C] Focus chain UA [auth K] Focus chain WA [auth L] Focus chain X [auth D] Focus chain XA [auth L] Focus chain Y [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain NA [auth I] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain T [auth C] Focus chain TA [auth K] Focus chain U [auth C] Focus chain UA [auth K] Focus chain WA [auth L] Focus chain X [auth D] Focus chain XA [auth L] Focus chain Y [auth D] Focus chain Z [auth E]

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, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.206 (Depositor), 0.202 (DCC)
R-Value Work: 0.193 (Depositor), 0.194 (DCC)
R-Value Observed: 0.193 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.638	α = 90
b = 165.372	β = 90.87
c = 125.789	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2019-11-20
Changes: Derived calculations
Version 1.3: 2019-12-25
Changes: Author supporting evidence
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-11-15
Changes: Data collection
Version 1.6: 2024-11-13
Changes: Structure summary