5JYB | pdb_00005jyb

Crystal structure of 3 mutant of Ba3275 (S116A, E243A, H313A), the member of S66 family of serine peptidases

PDB DOI: https://doi.org/10.2210/pdb5JYB/pdb

Classification: HYDROLASE
Organism(s): Bacillus cereus ATCC 10987
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-05-13 Released: 2016-06-15
Deposition Author(s): Nocek, B., Jedrzejczak, R., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.165 (Depositor), 0.166 (DCC)
R-Value Work:
0.140 (Depositor), 0.142 (DCC)
R-Value Observed:
0.141 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of 3 mutant of Ba3275 (S116A, E243A, H313A), the member of S66 family of serine peptidases

Nocek, B., Jedrzejczak, R., Joachimiak, A., CSGID

To be published.

Macromolecule Content

Total Structure Weight: 80.91 kDa
Atom Count: 6,377
Modeled Residue Count: 688
Deposited Residue Count: 692
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MccC family protein	A, B	346	Bacillus cereus ATCC 10987	Mutation(s): 3 Gene Names: BCE_3281
UniProt
Find proteins for Q734X3 (Bacillus cereus (strain ATCC 10987 / NRS 248)) Explore Q734X3 Go to UniProtKB: Q734X3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q734X3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain D [auth A]	D [auth A], K [auth B]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	E [auth A], L [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B] Focus chain J [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain H [auth A]	H [auth A], P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain P [auth B]
SBT Query on SBT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B]	G [auth A], O [auth B]	2-BUTANOL C₄ H₁₀ O BTANRVKWQNVYAZ-BYPYZUCNSA-N		Interactions Focus chain G [auth A] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain O [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B]	M [auth B], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.165 (Depositor), 0.166 (DCC)
R-Value Work: 0.140 (Depositor), 0.142 (DCC)
R-Value Observed: 0.141 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.444	α = 90
b = 71.225	β = 109.19
c = 82.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-06-15

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-06-15
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description