3CU3 | pdb_00003cu3

Crystal structure of a domain of unknown function with a cystatin-like fold (npun_r1993) from nostoc punctiforme pcc 73102 at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3CU3/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Nostoc punctiforme PCC 73102
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-04-15 Released: 2008-04-29 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal structure of Domain of Unknown Function with a Cystatin-like Fold (ZP_00107529.1) from Nostoc punctiforme PCC 73102 at 2.00 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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.74 kDa 
• Atom Count: 1,459 
• Modeled Residue Count: 162 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Domain of unknown function with a cystatin-like fold	A	172	Nostoc punctiforme PCC 73102	Mutation(s): 0  Gene Names: ZP_00107529.1
UniProt
Find proteins for D0VWT9 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102)) Explore D0VWT9  Go to UniProtKB:  D0VWT9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33CU3

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.51	α = 90
b = 71.9	β = 90
c = 117.56	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-29 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: 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
• Version 1.5: 2024-10-09
  Changes: Data collection, Structure summary