5C31 | pdb_00005c31

Constitutively active Sin recombinase catalytic domain reveals two rotational intermediates

PDB DOI: https://doi.org/10.2210/pdb5C31/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-06-16 Released: 2016-12-21
Deposition Author(s): Trejo, C.S., Rice, P.A.
Funding Organization(s): National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.286 (Depositor), 0.290 (DCC)
R-Value Work:
0.227 (Depositor), 0.230 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Snapshots of a molecular swivel in action

Trejo, C.S., Rock, R.S., Star, W.M., Boocock, M.R., Rice, P.A.

(2018) Nucleic Acids Res

DOI: https://doi.org/10.1093/nar/gkx1309

Macromolecule Content

Total Structure Weight: 183.83 kDa
Atom Count: 12,305
Modeled Residue Count: 1,501
Deposited Residue Count: 1,536
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sin, putative plasmid resolvase dimer	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	128	Staphylococcus aureus	Mutation(s): 2 Gene Names: Sin
UniProt
Find proteins for P20384 (Staphylococcus aureus) Explore P20384 Go to UniProtKB: P20384
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20384
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 Z [auth I] SDF format, chain Y [auth I] SDF format, chain X [auth H] SDF format, chain W [auth H] SDF format, chain V [auth H] SDF format, chain U [auth G] SDF format, chain T [auth F] SDF format, chain S [auth E] SDF format, chain R [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth A] SDF format, chain GA [auth L] SDF format, chain FA [auth L] SDF format, chain EA [auth K] SDF format, chain DA [auth J] SDF format, chain CA [auth J] SDF format, chain BA [auth I] SDF format, chain AA [auth I] MOL2 format, chain Z [auth I] MOL2 format, chain Y [auth I] MOL2 format, chain X [auth H] MOL2 format, chain W [auth H] MOL2 format, chain V [auth H] MOL2 format, chain U [auth G] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] MOL2 format, chain GA [auth L] MOL2 format, chain FA [auth L] MOL2 format, chain EA [auth K] MOL2 format, chain DA [auth J] MOL2 format, chain CA [auth J] MOL2 format, chain BA [auth I] MOL2 format, chain AA [auth I] mmCIF format, chain Z [auth I] mmCIF format, chain Y [auth I] mmCIF format, chain X [auth H] mmCIF format, chain W [auth H] mmCIF format, chain V [auth H] mmCIF format, chain U [auth G] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A] mmCIF format, chain GA [auth L] mmCIF format, chain FA [auth L] mmCIF format, chain EA [auth K] mmCIF format, chain DA [auth J] mmCIF format, chain CA [auth J] mmCIF format, chain BA [auth I] mmCIF format, chain AA [auth I]	AA [auth I] BA [auth I] CA [auth J] DA [auth J] EA [auth K] AA [auth I], BA [auth I], CA [auth J], DA [auth J], EA [auth K], FA [auth L], GA [auth L], M [auth A], N [auth B], O [auth B], P [auth C], Q [auth C], R [auth D], S [auth E], T [auth F], U [auth G], V [auth H], W [auth H], X [auth H], Y [auth I], Z [auth I]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth I] Focus chain BA [auth I] Focus chain CA [auth J] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth L] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth I] Focus chain BA [auth I] Focus chain CA [auth J] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain GA [auth L] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth I]

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: 3.10 Å
R-Value Free: 0.286 (Depositor), 0.290 (DCC)
R-Value Work: 0.227 (Depositor), 0.230 (DCC)
R-Value Observed: 0.230 (Depositor)

Diffraction Data: https://doi.org/10.15785/SBGRID/146

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.589	α = 90
b = 152.719	β = 90
c = 193.753	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-12-21

Deposition Author(s):

Trejo, C.S.

Rice, P.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)	United States	T32EB009412
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM086826
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM078450

Revision History (Full details and data files)

Version 1.0: 2016-12-21
Type: Initial release
Version 1.1: 2017-09-06
Changes: Author supporting evidence
Version 1.2: 2018-01-17
Changes: Database references
Version 1.3: 2019-12-11
Changes: Author supporting evidence
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Refinement description
Version 1.5: 2023-11-15
Changes: Data collection
Version 1.6: 2024-10-16
Changes: Structure summary

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Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 5C31 | pdb_00005c31

Constitutively active Sin recombinase catalytic domain reveals two rotational intermediates

Snapshots of a molecular swivel in action

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

5C31 | pdb_00005c31