5I1Z | pdb_00005i1z

Structure of nvPizza2-H16S58

PDB DOI: https://doi.org/10.2210/pdb5I1Z/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-02-07 Released: 2017-02-08
Deposition Author(s): Tame, J.R.H., Voet, A.R.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.187 (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

Broken Symmetry: Partial domain swapping in an artificial trimeric protein

Tame, J.R.H., Voet, A.R.D., Addy, C., Terada, D., Zhang, K.Y.J., Sekine, S.-I., Unzai, S., Kawano, R., Park, S.Y.

To be published.

Macromolecule Content

Total Structure Weight: 160.59 kDa
Atom Count: 12,233
Modeled Residue Count: 1,525
Deposited Residue Count: 1,566
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nvPizza2-H16S58	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	87	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 HA [auth M] SDF format, chain S [auth A] SDF format, chain Y [auth D] SDF format, chain Z [auth F] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain LA [auth P] SDF format, chain KA [auth P] SDF format, chain JA [auth O] SDF format, chain IA [auth N] SDF format, chain GA [auth L] SDF format, chain FA [auth L] SDF format, chain EA [auth J] SDF format, chain DA [auth I] SDF format, chain CA [auth G] SDF format, chain BA [auth G] SDF format, chain AA [auth G] MOL2 format, chain HA [auth M] MOL2 format, chain S [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth F] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain LA [auth P] MOL2 format, chain KA [auth P] MOL2 format, chain JA [auth O] MOL2 format, chain IA [auth N] MOL2 format, chain GA [auth L] MOL2 format, chain FA [auth L] MOL2 format, chain EA [auth J] MOL2 format, chain DA [auth I] MOL2 format, chain CA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth G] mmCIF format, chain HA [auth M] mmCIF format, chain S [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth F] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain LA [auth P] mmCIF format, chain KA [auth P] mmCIF format, chain JA [auth O] mmCIF format, chain IA [auth N] mmCIF format, chain GA [auth L] mmCIF format, chain FA [auth L] mmCIF format, chain EA [auth J] mmCIF format, chain DA [auth I] mmCIF format, chain CA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth G]	AA [auth G] BA [auth G] CA [auth G] DA [auth I] EA [auth J] AA [auth G], BA [auth G], CA [auth G], DA [auth I], EA [auth J], FA [auth L], GA [auth L], HA [auth M], IA [auth N], JA [auth O], KA [auth P], LA [auth P], S [auth A], T [auth C], U [auth C], V [auth D], W [auth D], X [auth D], Y [auth D], Z [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth I] Focus chain EA [auth J] Focus chain FA [auth L] Focus chain GA [auth L] Focus chain HA [auth M] Focus chain IA [auth N] Focus chain JA [auth O] Focus chain KA [auth P] Focus chain LA [auth P] Focus chain S [auth A] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth I] Focus chain EA [auth J] Focus chain FA [auth L] Focus chain GA [auth L] Focus chain HA [auth M] Focus chain IA [auth N] Focus chain JA [auth O] Focus chain KA [auth P] Focus chain LA [auth P] Focus chain S [auth A] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.186 (Depositor), 0.190 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.35	α = 90
b = 189.776	β = 90
c = 69.841	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-02-08

Deposition Author(s):

Tame, J.R.H.

Voet, A.R.D.

Revision History (Full details and data files)

Version 1.0: 2017-02-08
Type: Initial release
Version 1.1: 2020-02-19
Changes: Data collection
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description