3KDF | pdb_00003kdf

X-ray Crystal Structure of the Human Replication Protein A Complex from Wheat Germ Cell Free Expression

• PDB DOI: https://doi.org/10.2210/pdb3KDF/pdb

• Classification: REPLICATION
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2009-10-22 Released: 2009-12-01 
• Deposition Author(s): Burgie, E.S., Bingman, C.A., Phillips Jr., G.N., Fox, B.G., Makino, S.-I., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

X-ray Crystal Structure of the Human Replication Protein A Complex from Wheat Germ Cell Free Expression

Makino, S.-I., Burgie, E.S., Bingman, C.A., Fox, B.G., Phillips Jr., G.N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.95 kDa 
• Atom Count: 4,185 
• Modeled Residue Count: 470 
• Deposited Residue Count: 506 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication protein A 14 kDa subunit	A, C	121	Homo sapiens	Mutation(s): 1  Gene Names: REPA3, RPA14, RPA3
UniProt & NIH Common Fund Data Resources
Find proteins for P35244 (Homo sapiens) Explore P35244  Go to UniProtKB:  P35244
PHAROS:  P35244 GTEx:  ENSG00000106399

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication protein A 32 kDa subunit	B [auth D], D [auth B]	132	Homo sapiens	Mutation(s): 1  Gene Names: REPA2, RPA2, RPA32, RPA34
UniProt & NIH Common Fund Data Resources
Find proteins for P15927 (Homo sapiens) Explore P15927  Go to UniProtKB:  P15927
PHAROS:  P15927 GTEx:  ENSG00000117748

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth A], G [auth D], H [auth D], I [auth C], J [auth C], K [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.68	α = 90
b = 77.7	β = 90
c = 121.3	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-01 
Deposition Author(s): Burgie, E.S., Bingman, C.A., Phillips Jr., G.N., Fox, B.G., Makino, S.-I., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-27
  Changes: Data collection, Structure summary