4M65 | pdb_00004m65

In situ thermolysin crystallized on a MiTeGen micromesh with asparagine ligand

PDB DOI: https://doi.org/10.2210/pdb4M65/pdb

Classification: HYDROLASE
Organism(s): Thermus thermophilus
Mutation(s): No

Deposited: 2013-08-08 Released: 2013-10-30
Deposition Author(s): Yin, X., Scalia, A., Leroy, L., Cuttitta, C.M., Polizzo, G.M., Ericson, D.L., Roessler, C.G., Campos, O., Agarwal, R., Allaire, M., Orville, A.M., Jackimowicz, R., Ma, M.Y., Sweet, R.M., Soares, A.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.159 (Depositor), 0.168 (DCC)
R-Value Work:
0.130 (Depositor), 0.144 (DCC)
R-Value Observed:
0.132 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes

Yin, X., Scalia, A., Leroy, L., Cuttitta, C.M., Polizzo, G.M., Ericson, D.L., Roessler, C.G., Campos, O., Agarwal, R., Allaire, M., Orville, A.M., Jackimowicz, R., Ma, M.Y., Sweet, R.M., Soares, A.S.

(null) Acta Crystallogr D Biol Crystallogr D70: 1177-1189

Macromolecule Content

Total Structure Weight: 35.58 kDa
Atom Count: 3,009
Modeled Residue Count: 316
Deposited Residue Count: 317
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermolysin	A	317	Thermus thermophilus	Mutation(s): 0 EC: 3.4.24
UniProt
Find proteins for V5IRV7 (Thermus thermophilus) Explore V5IRV7 Go to UniProtKB: V5IRV7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	V5IRV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ASN Query on ASN Download:Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A] mmCIF format, chain U [auth A]	U [auth A]	ASPARAGINE C₄ H₈ N₂ O₃ DCXYFEDJOCDNAF-REOHCLBHSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain R [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain R [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain R [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A] K [auth A] L [auth A] M [auth A] N [auth A] J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
H2S Query on H2S Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A]	HYDROSULFURIC ACID H₂ S RWSOTUBLDIXVET-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.159 (Depositor), 0.168 (DCC)
R-Value Work: 0.130 (Depositor), 0.144 (DCC)
R-Value Observed: 0.132 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.831	α = 90
b = 92.831	β = 90
c = 129.171	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-10-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-30
Type: Initial release
Version 1.1: 2014-05-14
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description