6QPA | pdb_00006qpa

Halothiobacillus neapolitanus sulfur oxygenase reductase

PDB DOI: https://doi.org/10.2210/pdb6QPA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Halothiobacillus neapolitanus c2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-02-13 Released: 2020-03-18
Deposition Author(s): Frazao, C., Klezin, A., Poell, U., Veith, A., Ruehl, P., Coelho, R.
Funding Organization(s): Foundation for Science and Technology (FCT), German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.162 (Depositor), 0.162 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Multiple sulfane modifications in active-site cysteine thiols of two sulfur oxygenase reductases and analysis of substrate/product channels

Frazao, C., Klezin, A., Poell, U., Veith, A., Ruehl, P., Coelho, R.

To be published.

Macromolecule Content

Total Structure Weight: 855.66 kDa
Atom Count: 63,067
Modeled Residue Count: 7,439
Deposited Residue Count: 7,536
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfur oxygenase/reductase	A B C D E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S [auth T], T [auth U], U [auth V], V [auth W], W [auth Y], X [auth Z]	314	Halothiobacillus neapolitanus c2	Mutation(s): 0 Gene Names: Hneap_1222 EC: 1.13.11.55
UniProt
Find proteins for D0L035 (Halothiobacillus neapolitanus (strain ATCC 23641 / DSM 15147 / CIP 104769 / NCIMB 8539 / c2)) Explore D0L035 Go to UniProtKB: D0L035
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0L035
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain ZB [auth Q] SDF format, chain Z [auth A] SDF format, chain YB [auth Q] SDF format, chain YA [auth H] SDF format, chain XA [auth H] SDF format, chain WB [auth P] SDF format, chain VB [auth P] SDF format, chain VA [auth G] SDF format, chain UA [auth G] SDF format, chain TB [auth O] SDF format, chain SB [auth O] SDF format, chain SA [auth F] SDF format, chain RC [auth Z] SDF format, chain RA [auth F] SDF format, chain QB [auth N] SDF format, chain QA [auth F] SDF format, chain PC [auth Y] SDF format, chain PB [auth N] SDF format, chain OA [auth E] SDF format, chain NC [auth W] SDF format, chain NB [auth M] SDF format, chain NA [auth E] SDF format, chain MC [auth W] SDF format, chain MB [auth M] SDF format, chain LA [auth D] SDF format, chain KC [auth V] SDF format, chain KB [auth L] SDF format, chain KA [auth D] SDF format, chain JC [auth V] SDF format, chain JB [auth L] SDF format, chain IA [auth C] SDF format, chain HC [auth V] SDF format, chain HB [auth K] SDF format, chain HA [auth C] SDF format, chain GC [auth U] SDF format, chain GB [auth K] SDF format, chain GA [auth C] SDF format, chain FC [auth U] SDF format, chain EB [auth J] SDF format, chain EA [auth B] SDF format, chain DC [auth T] SDF format, chain DB [auth J] SDF format, chain DA [auth B] SDF format, chain BC [auth R] SDF format, chain BB [auth I] SDF format, chain BA [auth A] SDF format, chain AB [auth I] SDF format, chain AA [auth A] MOL2 format, chain ZB [auth Q] MOL2 format, chain Z [auth A] MOL2 format, chain YB [auth Q] MOL2 format, chain YA [auth H] MOL2 format, chain XA [auth H] MOL2 format, chain WB [auth P] MOL2 format, chain VB [auth P] MOL2 format, chain VA [auth G] MOL2 format, chain UA [auth G] MOL2 format, chain TB [auth O] MOL2 format, chain SB [auth O] MOL2 format, chain SA [auth F] MOL2 format, chain RC [auth Z] MOL2 format, chain RA [auth F] MOL2 format, chain QB [auth N] MOL2 format, chain QA [auth F] MOL2 format, chain PC [auth Y] MOL2 format, chain PB [auth N] MOL2 format, chain OA [auth E] MOL2 format, chain NC [auth W] MOL2 format, chain NB [auth M] MOL2 format, chain NA [auth E] MOL2 format, chain MC [auth W] MOL2 format, chain MB [auth M] MOL2 format, chain LA [auth D] MOL2 format, chain KC [auth V] MOL2 format, chain KB [auth L] MOL2 format, chain KA [auth D] MOL2 format, chain JC [auth V] MOL2 format, chain JB [auth L] MOL2 format, chain IA [auth C] MOL2 format, chain HC [auth V] MOL2 format, chain HB [auth K] MOL2 format, chain HA [auth C] MOL2 format, chain GC [auth U] MOL2 format, chain GB [auth K] MOL2 format, chain GA [auth C] MOL2 format, chain FC [auth U] MOL2 format, chain EB [auth J] MOL2 format, chain EA [auth B] MOL2 format, chain DC [auth T] MOL2 format, chain DB [auth J] MOL2 format, chain DA [auth B] MOL2 format, chain BC [auth R] MOL2 format, chain BB [auth I] MOL2 format, chain BA [auth A] MOL2 format, chain AB [auth I] MOL2 format, chain AA [auth A] mmCIF format, chain ZB [auth Q] mmCIF format, chain Z [auth A] mmCIF format, chain YB [auth Q] mmCIF format, chain YA [auth H] mmCIF format, chain XA [auth H] mmCIF format, chain WB [auth P] mmCIF format, chain VB [auth P] mmCIF format, chain VA [auth G] mmCIF format, chain UA [auth G] mmCIF format, chain TB [auth O] mmCIF format, chain SB [auth O] mmCIF format, chain SA [auth F] mmCIF format, chain RC [auth Z] mmCIF format, chain RA [auth F] mmCIF format, chain QB [auth N] mmCIF format, chain QA [auth F] mmCIF format, chain PC [auth Y] mmCIF format, chain PB [auth N] mmCIF format, chain OA [auth E] mmCIF format, chain NC [auth W] mmCIF format, chain NB [auth M] mmCIF format, chain NA [auth E] mmCIF format, chain MC [auth W] mmCIF format, chain MB [auth M] mmCIF format, chain LA [auth D] mmCIF format, chain KC [auth V] mmCIF format, chain KB [auth L] mmCIF format, chain KA [auth D] mmCIF format, chain JC [auth V] mmCIF format, chain JB [auth L] mmCIF format, chain IA [auth C] mmCIF format, chain HC [auth V] mmCIF format, chain HB [auth K] mmCIF format, chain HA [auth C] mmCIF format, chain GC [auth U] mmCIF format, chain GB [auth K] mmCIF format, chain GA [auth C] mmCIF format, chain FC [auth U] mmCIF format, chain EB [auth J] mmCIF format, chain EA [auth B] mmCIF format, chain DC [auth T] mmCIF format, chain DB [auth J] mmCIF format, chain DA [auth B] mmCIF format, chain BC [auth R] mmCIF format, chain BB [auth I] mmCIF format, chain BA [auth A] mmCIF format, chain AB [auth I] mmCIF format, chain AA [auth A]	AA [auth A] AB [auth I] BA [auth A] BB [auth I] BC [auth R] AA [auth A], AB [auth I], BA [auth A], BB [auth I], BC [auth R], DA [auth B], DB [auth J], DC [auth T], EA [auth B], EB [auth J], FC [auth U], GA [auth C], GB [auth K], GC [auth U], HA [auth C], HB [auth K], HC [auth V], IA [auth C], JB [auth L], JC [auth V], KA [auth D], KB [auth L], KC [auth V], LA [auth D], MB [auth M], MC [auth W], NA [auth E], NB [auth M], NC [auth W], OA [auth E], PB [auth N], PC [auth Y], QA [auth F], QB [auth N], RA [auth F], RC [auth Z], SA [auth F], SB [auth O], TB [auth O], UA [auth G], VA [auth G], VB [auth P], WB [auth P], XA [auth H], YA [auth H], YB [auth Q], Z [auth A], ZB [auth Q]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth A] Focus chain AB [auth I] Focus chain BA [auth A] Focus chain BB [auth I] Focus chain BC [auth R] Focus chain DA [auth B] Focus chain DB [auth J] Focus chain DC [auth T] Focus chain EA [auth B] Focus chain EB [auth J] Focus chain FC [auth U] Focus chain GA [auth C] Focus chain GB [auth K] Focus chain GC [auth U] Focus chain HA [auth C] Focus chain HB [auth K] Focus chain HC [auth V] Focus chain IA [auth C] Focus chain JB [auth L] Focus chain JC [auth V] Focus chain KA [auth D] Focus chain KB [auth L] Focus chain KC [auth V] Focus chain LA [auth D] Focus chain MB [auth M] Focus chain MC [auth W] Focus chain NA [auth E] Focus chain NB [auth M] Focus chain NC [auth W] Focus chain OA [auth E] Focus chain PB [auth N] Focus chain PC [auth Y] Focus chain QA [auth F] Focus chain QB [auth N] Focus chain RA [auth F] Focus chain RC [auth Z] Focus chain SA [auth F] Focus chain SB [auth O] Focus chain TB [auth O] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain VB [auth P] Focus chain WB [auth P] Focus chain XA [auth H] Focus chain YA [auth H] Focus chain YB [auth Q] Focus chain Z [auth A] Focus chain ZB [auth Q] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth I] Focus chain BA [auth A] Focus chain BB [auth I] Focus chain BC [auth R] Focus chain DA [auth B] Focus chain DB [auth J] Focus chain DC [auth T] Focus chain EA [auth B] Focus chain EB [auth J] Focus chain FC [auth U] Focus chain GA [auth C] Focus chain GB [auth K] Focus chain GC [auth U] Focus chain HA [auth C] Focus chain HB [auth K] Focus chain HC [auth V] Focus chain IA [auth C] Focus chain JB [auth L] Focus chain JC [auth V] Focus chain KA [auth D] Focus chain KB [auth L] Focus chain KC [auth V] Focus chain LA [auth D] Focus chain MB [auth M] Focus chain MC [auth W] Focus chain NA [auth E] Focus chain NB [auth M] Focus chain NC [auth W] Focus chain OA [auth E] Focus chain PB [auth N] Focus chain PC [auth Y] Focus chain QA [auth F] Focus chain QB [auth N] Focus chain RA [auth F] Focus chain RC [auth Z] Focus chain SA [auth F] Focus chain SB [auth O] Focus chain TB [auth O] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain VB [auth P] Focus chain WB [auth P] Focus chain XA [auth H] Focus chain YA [auth H] Focus chain YB [auth Q] Focus chain Z [auth A] Focus chain ZB [auth Q]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain ZA [auth I] SDF format, chain Y [auth A] SDF format, chain XB [auth Q] SDF format, chain WA [auth H] SDF format, chain UB [auth P] SDF format, chain TA [auth G] SDF format, chain RB [auth O] SDF format, chain QC [auth Z] SDF format, chain PA [auth F] SDF format, chain OC [auth Y] SDF format, chain OB [auth N] SDF format, chain MA [auth E] SDF format, chain LC [auth W] SDF format, chain LB [auth M] SDF format, chain JA [auth D] SDF format, chain IC [auth V] SDF format, chain IB [auth L] SDF format, chain FB [auth K] SDF format, chain FA [auth C] SDF format, chain EC [auth U] SDF format, chain CC [auth T] SDF format, chain CB [auth J] SDF format, chain CA [auth B] SDF format, chain AC [auth R] MOL2 format, chain ZA [auth I] MOL2 format, chain Y [auth A] MOL2 format, chain XB [auth Q] MOL2 format, chain WA [auth H] MOL2 format, chain UB [auth P] MOL2 format, chain TA [auth G] MOL2 format, chain RB [auth O] MOL2 format, chain QC [auth Z] MOL2 format, chain PA [auth F] MOL2 format, chain OC [auth Y] MOL2 format, chain OB [auth N] MOL2 format, chain MA [auth E] MOL2 format, chain LC [auth W] MOL2 format, chain LB [auth M] MOL2 format, chain JA [auth D] MOL2 format, chain IC [auth V] MOL2 format, chain IB [auth L] MOL2 format, chain FB [auth K] MOL2 format, chain FA [auth C] MOL2 format, chain EC [auth U] MOL2 format, chain CC [auth T] MOL2 format, chain CB [auth J] MOL2 format, chain CA [auth B] MOL2 format, chain AC [auth R] mmCIF format, chain ZA [auth I] mmCIF format, chain Y [auth A] mmCIF format, chain XB [auth Q] mmCIF format, chain WA [auth H] mmCIF format, chain UB [auth P] mmCIF format, chain TA [auth G] mmCIF format, chain RB [auth O] mmCIF format, chain QC [auth Z] mmCIF format, chain PA [auth F] mmCIF format, chain OC [auth Y] mmCIF format, chain OB [auth N] mmCIF format, chain MA [auth E] mmCIF format, chain LC [auth W] mmCIF format, chain LB [auth M] mmCIF format, chain JA [auth D] mmCIF format, chain IC [auth V] mmCIF format, chain IB [auth L] mmCIF format, chain FB [auth K] mmCIF format, chain FA [auth C] mmCIF format, chain EC [auth U] mmCIF format, chain CC [auth T] mmCIF format, chain CB [auth J] mmCIF format, chain CA [auth B] mmCIF format, chain AC [auth R]	AC [auth R] CA [auth B] CB [auth J] CC [auth T] EC [auth U] AC [auth R], CA [auth B], CB [auth J], CC [auth T], EC [auth U], FA [auth C], FB [auth K], IB [auth L], IC [auth V], JA [auth D], LB [auth M], LC [auth W], MA [auth E], OB [auth N], OC [auth Y], PA [auth F], QC [auth Z], RB [auth O], TA [auth G], UB [auth P], WA [auth H], XB [auth Q], Y [auth A], ZA [auth I]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AC [auth R] Focus chain CA [auth B] Focus chain CB [auth J] Focus chain CC [auth T] Focus chain EC [auth U] Focus chain FA [auth C] Focus chain FB [auth K] Focus chain IB [auth L] Focus chain IC [auth V] Focus chain JA [auth D] Focus chain LB [auth M] Focus chain LC [auth W] Focus chain MA [auth E] Focus chain OB [auth N] Focus chain OC [auth Y] Focus chain PA [auth F] Focus chain QC [auth Z] Focus chain RB [auth O] Focus chain TA [auth G] Focus chain UB [auth P] Focus chain WA [auth H] Focus chain XB [auth Q] Focus chain Y [auth A] Focus chain ZA [auth I] Interactions & Density Focus chain AC [auth R] Focus chain CA [auth B] Focus chain CB [auth J] Focus chain CC [auth T] Focus chain EC [auth U] Focus chain FA [auth C] Focus chain FB [auth K] Focus chain IB [auth L] Focus chain IC [auth V] Focus chain JA [auth D] Focus chain LB [auth M] Focus chain LC [auth W] Focus chain MA [auth E] Focus chain OB [auth N] Focus chain OC [auth Y] Focus chain PA [auth F] Focus chain QC [auth Z] Focus chain RB [auth O] Focus chain TA [auth G] Focus chain UB [auth P] Focus chain WA [auth H] Focus chain XB [auth Q] Focus chain Y [auth A] Focus chain ZA [auth I]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS Query on CSS	A B C D E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S [auth T], T [auth U], U [auth V], V [auth W], W [auth Y], X [auth Z]	L-PEPTIDE LINKING	C₃ H₇ N O₂ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.200 (Depositor), 0.200 (DCC)
R-Value Work: 0.162 (Depositor), 0.162 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.84	α = 90
b = 212.45	β = 90
c = 215.98	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-03-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Foundation for Science and Technology (FCT)	Portugal	LIOA-01-0145-FEDER-007660
German Research Foundation (DFG)	Germany	Kl885-6/1
German Research Foundation (DFG)	Germany	Kl885-7/1

Revision History (Full details and data files)

Version 1.0: 2020-03-18
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary