3QFH | pdb_00003qfh

2.05 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (EpiP) from Staphylococcus aureus.

PDB DOI: https://doi.org/10.2210/pdb3QFH/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus subsp. aureus COL
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-01-21 Released: 2011-02-02
Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.216 (Depositor), 0.230 (DCC)
R-Value Work:
0.170 (Depositor), 0.182 (DCC)
R-Value Observed:
0.172 (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

2.05 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (EpiP) from Staphylococcus aureus.

Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Bagnoli, F., Falugi, F., Bottomley, M., Grandi, G., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 403.93 kDa
Atom Count: 28,510
Modeled Residue Count: 3,395
Deposited Residue Count: 3,576
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermin leader peptide processing serine protease EpiP	A, B, C, D, E A, B, C, D, E, F, G, H	447	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0 Gene Names: epiP, SACOL1874 EC: 3.4.21
UniProt
Find proteins for A0A0H2WX20 (Staphylococcus aureus (strain COL)) Explore A0A0H2WX20 Go to UniProtKB: A0A0H2WX20
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2WX20
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 C] SDF format, chain AB [auth H] SDF format, chain BA [auth C] SDF format, chain BB [auth H] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain L [auth A] SDF format, chain MA [auth E] SDF format, chain N [auth A] SDF format, chain NA [auth F] SDF format, chain O [auth A] SDF format, chain OA [auth F] SDF format, chain P [auth A] SDF format, chain PA [auth F] SDF format, chain QA [auth F] SDF format, chain RA [auth G] SDF format, chain S [auth B] SDF format, chain SA [auth G] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain WA [auth H] SDF format, chain X [auth B] SDF format, chain XA [auth H] SDF format, chain Y [auth C] SDF format, chain YA [auth H] SDF format, chain Z [auth C] SDF format, chain ZA [auth H] SDF format, chain UA [auth G] SDF format, chain TA [auth G] SDF format, chain M [auth A] SDF format, chain LA [auth E] SDF format, chain KA [auth E] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth H] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain QA [auth F] MOL2 format, chain RA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth G] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth H] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth H] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth H] MOL2 format, chain UA [auth G] MOL2 format, chain TA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain KA [auth E] mmCIF format, chain AA [auth C] mmCIF format, chain AB [auth H] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth H] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth F] mmCIF format, chain QA [auth F] mmCIF format, chain RA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth G] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth H] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth H] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth H] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth H] mmCIF format, chain UA [auth G] mmCIF format, chain TA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain KA [auth E]	AA [auth C] AB [auth H] BA [auth C] BB [auth H] DA [auth D] AA [auth C], AB [auth H], BA [auth C], BB [auth H], DA [auth D], EA [auth D], FA [auth D], GA [auth D], IA [auth E], JA [auth E], KA [auth E], L [auth A], LA [auth E], M [auth A], MA [auth E], N [auth A], NA [auth F], O [auth A], OA [auth F], P [auth A], PA [auth F], QA [auth F], RA [auth G], S [auth B], SA [auth G], T [auth B], TA [auth G], U [auth B], UA [auth G], V [auth B], W [auth B], WA [auth H], X [auth B], XA [auth H], Y [auth C], YA [auth H], Z [auth C], ZA [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain AB [auth H] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth A] Focus chain OA [auth F] Focus chain P [auth A] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain RA [auth G] Focus chain S [auth B] Focus chain SA [auth G] Focus chain T [auth B] Focus chain TA [auth G] Focus chain U [auth B] Focus chain UA [auth G] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth H] Focus chain X [auth B] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth H] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain MA [auth E] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth A] Focus chain OA [auth F] Focus chain P [auth A] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain RA [auth G] Focus chain S [auth B] Focus chain SA [auth G] Focus chain T [auth B] Focus chain TA [auth G] Focus chain U [auth B] Focus chain UA [auth G] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth H] Focus chain X [auth B] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain HA [auth E] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain HA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain HA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	HA [auth E], K [auth A], Q [auth B], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain HA [auth E] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain HA [auth E] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain I [auth A] SDF format, chain VA [auth H] MOL2 format, chain CA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain VA [auth H] mmCIF format, chain CA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain VA [auth H]	CA [auth D], I [auth A], VA [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain I [auth A] Focus chain VA [auth H] Interactions & Density Focus chain CA [auth D] Focus chain I [auth A] Focus chain VA [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.216 (Depositor), 0.230 (DCC)
R-Value Work: 0.170 (Depositor), 0.182 (DCC)
R-Value Observed: 0.172 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.505	α = 89.98
b = 94.696	β = 90.37
c = 122.999	γ = 116.79

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-02-02

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-02-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary