6MQL | pdb_00006mql

Crystal Structure of GTPase Domain of Human Septin 12 Mutant T89M

• PDB DOI: https://doi.org/10.2210/pdb6MQL/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-10-10 Released: 2019-11-20 
• Deposition Author(s): Castro, D.K.S.V., Pereira, H.M., Brandao-Neto, J., Ulian, A.P.U., Garratt, R.C.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of GTPase Domain of Human Septin 12

Castro, D.K.S.V., Pereira, H.M., Brandao-Neto, J., Ulian, A.P.U., Garratt, R.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.59 kDa 
• Atom Count: 2,169 
• Modeled Residue Count: 263 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Septin-12	A	295	Homo sapiens	Mutation(s): 1  Gene Names: SEPT12
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYM1 (Homo sapiens) Explore Q8IYM1  Go to UniProtKB:  Q8IYM1
PHAROS:  Q8IYM1 GTEx:  ENSG00000140623

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.92	α = 90
b = 56.49	β = 114.86
c = 70.29	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Castro, D.K.S.V., Pereira, H.M., Brandao-Neto, J., Ulian, A.P.U., Garratt, R.C.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2014/15546-1
Sao Paulo Research Foundation (FAPESP)	Brazil	2016/19734-2

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description