3G16

Crystal structure of protein of unknown function with cystatin-like fold (YP_001022489.1) from METHYLOBIUM PETROLEOPHILUM PM1 at 1.45 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3G16/pdb

• Classification: structural genomics, unknown function
• Organism(s): Methylibium petroleiphilum PM1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-29 Released: 2009-02-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.167 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 

Literature

Crystal structure of protein of unknown function with cystatin-like fold (YP_001022489.1) from METHYLOBIUM PETROLEOPHILUM PM1 at 1.45 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 35.27 kDa 
• Atom Count: 2,908 
• Modelled Residue Count: 308 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein with cystatin-like fold	A, B	156	Methylibium petroleiphilum PM1	Mutation(s): 0  Gene Names: Mpe_A3301, YP_001022489.1
UniProt
Find proteins for A2SL15 (Methylibium petroleiphilum (strain ATCC BAA-1232 / LMG 22953 / PM1)) Explore A2SL15  Go to UniProtKB:  A2SL15

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL	C [auth A], I [auth B]	Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.167 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M33G16

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.56	α = 90
b = 68.45	β = 90
c = 107.46	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations