4HC3 | pdb_00004hc3

Crystal structure of PpcA V13T mutant

• PDB DOI: https://doi.org/10.2210/pdb4HC3/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Geobacter sulfurreducens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-09-28 Released: 2012-10-31 
• Deposition Author(s): Pokkuluri, P.R., Schiffer, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.233 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

V13 mutants of PpcA

Pokkuluri, P.R., Schiffer, M.

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 10.29 kDa 
• Atom Count: 781 
• Modeled Residue Count: 71 
• Deposited Residue Count: 71 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PpcA	A	71	Geobacter sulfurreducens	Mutation(s): 1  Gene Names: ppcA
UniProt
Find proteins for Q8GGK7 (Geobacter sulfurreducens) Explore Q8GGK7  Go to UniProtKB:  Q8GGK7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	B [auth A], C [auth A], D [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
DXC	E [auth A]	(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID C24 H40 O4 KXGVEGMKQFWNSR-LLQZFEROSA-N
SO4	F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.233 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.4	α = 90
b = 32.4	β = 90
c = 178.4	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-31 
Deposition Author(s): Pokkuluri, P.R., Schiffer, M.

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Advisory, Data collection, Derived calculations, Refinement description
• Version 2.0: 2021-03-10
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-20
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 2.2: 2024-11-06
  Changes: Structure summary