3CNE | pdb_00003cne

Crystal structure of the putative protease I from Bacteroides thetaiotaomicron

PDB DOI: https://doi.org/10.2210/pdb3CNE/pdb

Classification: HYDROLASE
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2008-03-25 Released: 2008-04-15
Deposition Author(s): Zhang, R., Volkart, L., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.234 (Depositor), 0.243 (DCC)
R-Value Work:
0.186 (Depositor)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The crystal structure of the putative protease I from Bacteroides thetaiotaomicron.

Zhang, R., Volkart, L., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 79.51 kDa
Atom Count: 5,760
Modeled Residue Count: 695
Deposited Residue Count: 700
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative protease I	A, B, C, D	175	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: GI:29338570, BT_1263
UniProt
Find proteins for Q8A8A4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A8A4 Go to UniProtKB: Q8A8A4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8A8A4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain N [auth D] MOL2 format, chain I [auth B] MOL2 format, chain N [auth D] mmCIF format, chain I [auth B] mmCIF format, chain N [auth D]	I [auth B], N [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain I [auth B] Focus chain N [auth D] Interactions & Density Focus chain I [auth B] Focus chain N [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], J [auth C], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain M [auth D] SDF format, chain K [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C]	F [auth A], H [auth B], K [auth C], M [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.234 (Depositor), 0.243 (DCC)
R-Value Work: 0.186 (Depositor)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.607	α = 90
b = 68.021	β = 109.81
c = 75.389	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-04-15

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-04-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

3CNE | pdb_00003cne

Crystal structure of the putative protease I from Bacteroides thetaiotaomicron

Literature

The crystal structure of the putative protease I from Bacteroides thetaiotaomicron.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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