3MML | pdb_00003mml

Allophanate Hydrolase Complex from Mycobacterium smegmatis, Msmeg0435-Msmeg0436

PDB DOI: https://doi.org/10.2210/pdb3MML/pdb

Classification: HYDROLASE
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-04-20 Released: 2010-04-28
Deposition Author(s): Kaufmann, M., Chernishof, I., Shin, A., Germano, D., Sawaya, M.R., Waldo, G.S., Arbing, M.A., Perry, J., Eisenberg, D., Integrated Center for Structure and Function Innovation (ISFI), TB Structural Genomics Consortium (TBSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.202 (Depositor), 0.204 (DCC)
R-Value Work:
0.169 (Depositor), 0.169 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Allphanate Hydrolase Complex from M. smegmatis, Msmeg0435-Msmeg0436

Kaufmann, M., Chernishof, I., Shin, A., Germano, D., Sawaya, M.R., Waldo, G.S., Arbing, M.A., Perry, J., Eisenberg, D.

To be published.

Macromolecule Content

Total Structure Weight: 236.05 kDa
Atom Count: 15,919
Modeled Residue Count: 1,997
Deposited Residue Count: 2,184
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Allophanate hydrolase subunit 2	A, C, E, G	318	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: Msmeg0435, MSMEG_0435 EC: 3.5.1.54
UniProt
Find proteins for A0QPL0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QPL0 Go to UniProtKB: A0QPL0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0QPL0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Allophanate hydrolase subunit 1	B, D, F, H	228	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: Msmeg0436, MSMEG_0436
UniProt
Find proteins for A0QPL1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QPL1 Go to UniProtKB: A0QPL1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0QPL1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.202 (Depositor), 0.204 (DCC)
R-Value Work: 0.169 (Depositor), 0.169 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.483	α = 90
b = 84.239	β = 90
c = 402.075	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
TNT	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
BUSTER	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-04-28

Deposition Author(s):

Integrated Center for Structure and Function Innovation (ISFI)

TB Structural Genomics Consortium (TBSGC)

Revision History (Full details and data files)

Version 1.0: 2010-04-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary