2R9G | pdb_00002r9g

Crystal structure of the C-terminal fragment of AAA ATPase from Enterococcus faecium

PDB DOI: https://doi.org/10.2210/pdb2R9G/pdb

Classification: HYDROLASE
Organism(s): Enterococcus faecium DO
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-09-12 Released: 2007-10-02
Deposition Author(s): Ramagopal, U.A., Patskovsky, Y., Bonanno, J.B., Shi, W., Toro, R., Meyer, A.J., Rutter, M., Wu, B., Groshong, C., Gheyi, T., 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: 2.09 Å
R-Value Free:
0.248 (Depositor), 0.244 (DCC)
R-Value Work:
0.197 (Depositor), 0.198 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the C-Terminal Domain of AAA ATPase from Enterococcus faecium.

Ramagopal, U.A., Patskovsky, Y., Bonanno, J.B., Shi, W., Toro, R., Meyer, A.J., Rutter, M., Wu, B., Groshong, C., Gheyi, T., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 364.59 kDa
Atom Count: 24,661
Modeled Residue Count: 2,893
Deposited Residue Count: 3,264
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AAA ATPase, central region	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	204	Enterococcus faecium DO	Mutation(s): 0 Gene Names: EfaeDRAFT_0938
UniProt
Find proteins for I3U4Y0 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)) Explore I3U4Y0 Go to UniProtKB: I3U4Y0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I3U4Y0
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 Y [auth J] SDF format, chain X [auth H] SDF format, chain V [auth E] SDF format, chain FA [auth P] MOL2 format, chain Y [auth J] MOL2 format, chain X [auth H] MOL2 format, chain V [auth E] MOL2 format, chain FA [auth P] mmCIF format, chain Y [auth J] mmCIF format, chain X [auth H] mmCIF format, chain V [auth E] mmCIF format, chain FA [auth P]	FA [auth P], V [auth E], X [auth H], Y [auth J]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth P] Focus chain V [auth E] Focus chain X [auth H] Focus chain Y [auth J] Interactions & Density Focus chain FA [auth P] Focus chain V [auth E] Focus chain X [auth H] Focus chain Y [auth J]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Z [auth K] SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain T [auth E] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth B] SDF format, chain EA [auth P] SDF format, chain DA [auth O] SDF format, chain CA [auth O] SDF format, chain BA [auth L] SDF format, chain AA [auth L] MOL2 format, chain Z [auth K] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain T [auth E] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain EA [auth P] MOL2 format, chain DA [auth O] MOL2 format, chain CA [auth O] MOL2 format, chain BA [auth L] MOL2 format, chain AA [auth L] mmCIF format, chain Z [auth K] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain T [auth E] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain EA [auth P] mmCIF format, chain DA [auth O] mmCIF format, chain CA [auth O] mmCIF format, chain BA [auth L] mmCIF format, chain AA [auth L]	AA [auth L] BA [auth L] CA [auth O] DA [auth O] EA [auth P] AA [auth L], BA [auth L], CA [auth O], DA [auth O], EA [auth P], Q [auth B], R [auth C], S [auth C], T [auth E], U [auth E], W [auth F], Z [auth K]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth L] Focus chain BA [auth L] Focus chain CA [auth O] Focus chain DA [auth O] Focus chain EA [auth P] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth K] Interactions & Density Focus chain AA [auth L] Focus chain BA [auth L] Focus chain CA [auth O] Focus chain DA [auth O] Focus chain EA [auth P] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.248 (Depositor), 0.244 (DCC)
R-Value Work: 0.197 (Depositor), 0.198 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.778	α = 90.01
b = 103.39	β = 88.69
c = 103.374	γ = 86.05

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-10-02

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-10-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2018-11-14
Changes: Data collection, Structure summary
Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Refinement description