4QSZ | pdb_00004qsz

Crystal structure of mouse JMJd7 fused with maltose-binding protein

• PDB DOI: https://doi.org/10.2210/pdb4QSZ/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli K-12, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-06 Released: 2015-07-08 
• Deposition Author(s): Liu, H., Wang, C., Zhang, G.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 
  0.264 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Crystal structure of mouse JMJd7 fused with maltose-binding protein

Liu, H., Zhang, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 154.21 kDa 
• Atom Count: 10,832 
• Modeled Residue Count: 1,368 
• Deposited Residue Count: 1,374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein, JmjC domain-containing protein 7 chimera	A, B	687	Escherichia coli K-12, Mus musculus This entity is chimeric	Mutation(s): 0  Gene Names: malE, b4034, JW3994, Jmjd7 EC: 3.4 (UniProt), 1.14.11.63 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for P0C872 (Mus musculus) Explore P0C872  Go to UniProtKB:  P0C872
IMPC:  MGI:3845785
UniProt Groups	P0C872P0AEX9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	E [auth A], H [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
GLC	C [auth A], D [auth A], F [auth B], G [auth B]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free:  0.264 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.09	α = 90
b = 158.92	β = 94.08
c = 100.01	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-08 
Deposition Author(s): Liu, H., Wang, C., Zhang, G.Y.

Revision History  

• Version 1.0: 2015-07-08
  Type: Initial release
  
• Version 1.1: 2017-07-26
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary