4HI2 | pdb_00004hi2

Crystal structure of an Acylphosphatase protein cage

PDB DOI: https://doi.org/10.2210/pdb4HI2/pdb

Classification: HYDROLASE
Organism(s): Vibrio cholerae O395
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-10-11 Released: 2013-09-25
Deposition Author(s): Nath, S., Banerjee, R., Sen, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.289 (Depositor), 0.281 (DCC)
R-Value Work:
0.221 (Depositor), 0.226 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of acylphosphatase C20R mutant from Vibrio cholerae0395

Nath, S., Banerjee, R., Sen, U.

(2013) J Mol Biology

Macromolecule Content

Total Structure Weight: 126.99 kDa
Atom Count: 8,548
Modeled Residue Count: 1,058
Deposited Residue Count: 1,092
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acylphosphatase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	91	Vibrio cholerae O395	Mutation(s): 0 Gene Names: acyP, VC0395_A0969, VC395_1474 EC: 3.6.1.7
UniProt
Find proteins for A5F8G9 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F8G9 Go to UniProtKB: A5F8G9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5F8G9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth L] SDF format, chain BA [auth D] SDF format, chain BB [auth L] SDF format, chain CA [auth E] SDF format, chain CB [auth L] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain LA [auth G] SDF format, chain M [auth A] SDF format, chain MA [auth G] SDF format, chain N [auth A] SDF format, chain NA [auth H] SDF format, chain O [auth A] SDF format, chain OA [auth H] SDF format, chain P [auth A] SDF format, chain PA [auth H] SDF format, chain Q [auth B] SDF format, chain QA [auth I] SDF format, chain R [auth B] SDF format, chain RA [auth I] SDF format, chain S [auth B] SDF format, chain SA [auth I] SDF format, chain T [auth B] SDF format, chain TA [auth J] SDF format, chain U [auth B] SDF format, chain UA [auth J] SDF format, chain V [auth C] SDF format, chain VA [auth J] SDF format, chain W [auth C] SDF format, chain WA [auth J] SDF format, chain X [auth C] SDF format, chain XA [auth K] SDF format, chain Y [auth C] SDF format, chain YA [auth K] SDF format, chain Z [auth D] SDF format, chain ZA [auth K] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth L] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth L] MOL2 format, chain CA [auth E] MOL2 format, chain CB [auth L] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth I] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth I] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth I] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth J] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth J] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth J] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth J] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth K] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth K] MOL2 format, chain Z [auth D] MOL2 format, chain ZA [auth K] mmCIF format, chain AA [auth D] mmCIF format, chain AB [auth L] mmCIF format, chain BA [auth D] mmCIF format, chain BB [auth L] mmCIF format, chain CA [auth E] mmCIF format, chain CB [auth L] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain LA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth H] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth H] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth H] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth I] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth I] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth I] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth J] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth J] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth J] mmCIF format, chain W [auth C] mmCIF format, chain WA [auth J] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth K] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth K] mmCIF format, chain Z [auth D] mmCIF format, chain ZA [auth K]	AA [auth D] AB [auth L] BA [auth D] BB [auth L] CA [auth E] AA [auth D], AB [auth L], BA [auth D], BB [auth L], CA [auth E], CB [auth L], DA [auth E], EA [auth E], FA [auth E], GA [auth F], HA [auth F], IA [auth F], JA [auth G], KA [auth G], LA [auth G], M [auth A], MA [auth G], N [auth A], NA [auth H], O [auth A], OA [auth H], P [auth A], PA [auth H], Q [auth B], QA [auth I], R [auth B], RA [auth I], S [auth B], SA [auth I], T [auth B], TA [auth J], U [auth B], UA [auth J], V [auth C], VA [auth J], W [auth C], WA [auth J], X [auth C], XA [auth K], Y [auth C], YA [auth K], Z [auth D], ZA [auth K]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain AB [auth L] Focus chain BA [auth D] Focus chain BB [auth L] Focus chain CA [auth E] Focus chain CB [auth L] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain NA [auth H] Focus chain O [auth A] Focus chain OA [auth H] Focus chain P [auth A] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain QA [auth I] Focus chain R [auth B] Focus chain RA [auth I] Focus chain S [auth B] Focus chain SA [auth I] Focus chain T [auth B] Focus chain TA [auth J] Focus chain U [auth B] Focus chain UA [auth J] Focus chain V [auth C] Focus chain VA [auth J] Focus chain W [auth C] Focus chain WA [auth J] Focus chain X [auth C] Focus chain XA [auth K] Focus chain Y [auth C] Focus chain YA [auth K] Focus chain Z [auth D] Focus chain ZA [auth K] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth L] Focus chain BA [auth D] Focus chain BB [auth L] Focus chain CA [auth E] Focus chain CB [auth L] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain NA [auth H] Focus chain O [auth A] Focus chain OA [auth H] Focus chain P [auth A] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain QA [auth I] Focus chain R [auth B] Focus chain RA [auth I] Focus chain S [auth B] Focus chain SA [auth I] Focus chain T [auth B] Focus chain TA [auth J] Focus chain U [auth B] Focus chain UA [auth J] Focus chain V [auth C] Focus chain VA [auth J] Focus chain W [auth C] Focus chain WA [auth J] Focus chain X [auth C] Focus chain XA [auth K] Focus chain Y [auth C] Focus chain YA [auth K] Focus chain Z [auth D] Focus chain ZA [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.289 (Depositor), 0.281 (DCC)
R-Value Work: 0.221 (Depositor), 0.226 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.94	α = 90
b = 104.94	β = 90
c = 147.811	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-09-25

Deposition Author(s):

Nath, S.

Banerjee, R.

Sen, U.

Revision History (Full details and data files)

Version 1.0: 2013-09-25
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary