5A62 | pdb_00005a62

Hydrolytic potential of the ammonia-oxidizing Thaumarchaeon Nitrososphaera gargenis - crystal structure and activity profiles of carboxylesterases linked to their metabolic function

PDB DOI: https://doi.org/10.2210/pdb5A62/pdb

Classification: HYDROLASE
Organism(s): Candidatus Nitrososphaera gargensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-06-24 Released: 2016-07-06
Deposition Author(s): Chow, J., Kaljunen, H., Nittinger, E., Spieck, E., Rarey, M., Mueller-Dieckmann, J., Streit, W.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.163 (Depositor), 0.172 (DCC)
R-Value Work:
0.142 (Depositor), 0.153 (DCC)
R-Value Observed:
0.143 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Hydrolytic Potential of the Ammonia-Oxidizing Thaumarchaeon Nitrososphaera Gargenis - Crystal Structure and Activity Profiles of Carboxylesterases Linked to Their Metabolic Function

Chow, J., Kaljunen, H., Nittinger, E., Spieck, E., Rarey, M., Mueller-Dieckmann, J., Streit, W.R.

To be published.

Macromolecule Content

Total Structure Weight: 31.19 kDa
Atom Count: 2,431
Modeled Residue Count: 272
Deposited Residue Count: 277
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE ALPHA/BETA HYDROLASE FOLD PROTEIN	A	277	Candidatus Nitrososphaera gargensis	Mutation(s): 0
UniProt
Find proteins for K0IM51 (Nitrososphaera gargensis (strain Ga9.2)) Explore K0IM51 Go to UniProtKB: K0IM51
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K0IM51
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.163 (Depositor), 0.172 (DCC)
R-Value Work: 0.142 (Depositor), 0.153 (DCC)
R-Value Observed: 0.143 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.947	α = 90
b = 65.461	β = 104.17
c = 84.591	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-07-06

Deposition Author(s):

Mueller-Dieckmann, J.

Revision History (Full details and data files)

Version 1.0: 2016-07-06
Type: Initial release
Version 1.1: 2018-03-07
Changes: Data collection, Source and taxonomy
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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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.