6SWV | pdb_00006swv

Trypsin fast data collection

PDB DOI: https://doi.org/10.2210/pdb6SWV/pdb

Classification: HYDROLASE
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2019-09-24 Released: 2020-05-20
Deposition Author(s): von Stetten, D., Mueller-Dieckmann, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.206 (Depositor), 0.206 (DCC)
R-Value Work:
0.185 (Depositor), 0.185 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

ID30A-3 (MASSIF-3) - a beamline for macromolecular crystallography at the ESRF with a small intense beam.

von Stetten, D., Carpentier, P., Flot, D., Beteva, A., Caserotto, H., Dobias, F., Guijarro, M., Giraud, T., Lentini, M., McSweeney, S., Royant, A., Petitdemange, S., Sinoir, J., Surr, J., Svensson, O., Theveneau, P., Leonard, G.A., Mueller-Dieckmann, C.

(2020) J Synchrotron Radiat 27: 844-851

PubMed: 32381789 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1600577520004002
Primary Citation Related Structures:
6SWV, 6Y8G

PubMed Abstract:
ID30A-3 (or MASSIF-3) is a mini-focus (beam size 18 µm × 14 µm) highly intense (2.0 × 10 ¹³ photons s ^-1), fixed-energy (12.81 keV) beamline for macromolecular crystallography (MX) experiments at the European Synchrotron Radiation Facility (ESRF). MASSIF-3 is one of two fixed-energy beamlines sited on the first branch of the canted undulator setup on the ESRF ID30 port and is equipped with a MD2 micro-diffractometer, a Flex HCD sample changer, and an Eiger X 4M fast hybrid photon-counting detector. MASSIF-3 is recommended for collecting diffraction data from single small crystals (≤15 µm in one dimension) or for experiments using serial methods. The end-station has been in full user operation since December 2014, and here its current characteristics and capabilities are described.

Organizational Affiliation

European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France.

Macromolecule Content

Total Structure Weight: 26.54 kDa
Atom Count: 1,901
Modeled Residue Count: 223
Deposited Residue Count: 246
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cationic trypsin	A [auth AAA]	246	Bos taurus	Mutation(s): 0 EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760 Go to UniProtKB: P00760
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEN Query on BEN Download:Ideal Coordinates CCD File SDF format, chain I [auth AAA] MOL2 format, chain I [auth AAA] mmCIF format, chain I [auth AAA]	I [auth AAA]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain I [auth AAA] Interactions & Density Focus chain I [auth AAA]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth AAA] SDF format, chain G [auth AAA] SDF format, chain F [auth AAA] SDF format, chain E [auth AAA] SDF format, chain D [auth AAA] SDF format, chain C [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA] D [auth AAA] E [auth AAA] F [auth AAA] G [auth AAA] C [auth AAA], D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain H [auth AAA]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth AAA] MOL2 format, chain B [auth AAA] mmCIF format, chain B [auth AAA]	B [auth AAA]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth AAA] Interactions & Density Focus chain B [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.206 (Depositor), 0.206 (DCC)
R-Value Work: 0.185 (Depositor), 0.185 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.28	α = 90
b = 57.944	β = 90
c = 66.947	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-05-20

Deposition Author(s):

von Stetten, D.

Mueller-Dieckmann, C.

Revision History (Full details and data files)

Version 1.0: 2020-05-20
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