3LMC | pdb_00003lmc

Crystal Structure of zinc-dependent peptidase from Methanocorpusculum labreanum (strain Z), Northeast Structural Genomics Consortium Target MuR16

PDB DOI: https://doi.org/10.2210/pdb3LMC/pdb

Classification: HYDROLASE
Organism(s): Methanocorpusculum labreanum Z
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-01-29 Released: 2010-02-16
Deposition Author(s): Kuzin, A., Ashok, S., Vorobiev, S., Seetharaman, J., Patel, P., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.258 (Depositor), 0.250 (DCC)
R-Value Work:
0.212 (Depositor)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target MuR16

Kuzin, A., Ashok, S., Vorobiev, S., Seetharaman, J., Patel, P., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 24.68 kDa
Atom Count: 1,651
Modeled Residue Count: 191
Deposited Residue Count: 210
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase, zinc-dependent	A	210	Methanocorpusculum labreanum Z	Mutation(s): 0 Gene Names: Mlab_0438
UniProt
Find proteins for A2SQK8 (Methanocorpusculum labreanum (strain ATCC 43576 / DSM 4855 / Z)) Explore A2SQK8 Go to UniProtKB: A2SQK8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A2SQK8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.258 (Depositor), 0.250 (DCC)
R-Value Work: 0.212 (Depositor)
R-Value Observed: 0.214 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.627	α = 90
b = 60.889	β = 101.19
c = 47.859	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-02-16

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-02-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-11-16
Changes: Atomic model
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2018-01-24
Changes: Database references, Structure summary
Version 1.5: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary