6J8O | pdb_00006j8o

Structure of a hypothetical protease

• PDB DOI: https://doi.org/10.2210/pdb6J8O/pdb

• Classification: PEPTIDE BINDING PROTEIN/HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-01-20 Released: 2020-01-22 
• Deposition Author(s): Liao, S., Gao, J., Xu, C.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Structure of a hypothetical protease

Liao, S., Gao, J., Xu, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.26 kDa 
• Atom Count: 2,607 
• Modeled Residue Count: 272 
• Deposited Residue Count: 295 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Small vasohibin-binding protein	A	49	Homo sapiens	Mutation(s): 0  Gene Names: SVBP, CCDC23
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N300 (Homo sapiens) Explore Q8N300  Go to UniProtKB:  Q8N300
PHAROS:  Q8N300 GTEx:  ENSG00000177868

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulinyl-Tyr carboxypeptidase 1	B	238	Homo sapiens	Mutation(s): 0  Gene Names: VASH1, KIAA1036, VASH EC: 3.4.17.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L8A9 (Homo sapiens) Explore Q7L8A9  Go to UniProtKB:  Q7L8A9
PHAROS:  Q7L8A9 GTEx:  ENSG00000071246

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
8-mer peptide	C	8	Homo sapiens	Mutation(s): 0  EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P68363 (Homo sapiens) Explore P68363  Go to UniProtKB:  P68363
PHAROS:  P68363 GTEx:  ENSG00000123416

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.641	α = 90
b = 127.36	β = 90
c = 44.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-22 
Deposition Author(s): Liao, S., Gao, J., Xu, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31500601
National Natural Science Foundation of China	China	31570737
National Natural Science Foundation of China	China	31770806

Revision History  

• Version 1.0: 2020-01-22
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references
• Version 1.2: 2024-04-03
  Changes: Refinement description