3IPI | pdb_00003ipi

Crystal Structure of a Geranyltranstransferase from the Methanosarcina mazei

• PDB DOI: https://doi.org/10.2210/pdb3IPI/pdb

• Classification: TRANSFERASE
• Organism(s): Methanosarcina mazei
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-17 Released: 2009-09-08 
• Deposition Author(s): Kumaran, D., Mohammed, M.B., Brown, A., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.251 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Crystal Structure of a Geranyltranstransferase from the Methanosarcina mazei

Kumaran, D., Mohammed, M.B., Brown, A., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.92 kDa 
• Atom Count: 2,214 
• Modeled Residue Count: 268 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranyltranstransferase	A	295	Methanosarcina mazei	Mutation(s): 0  Gene Names: MM_0789 EC: 2.5.1 (PDB Primary Data), 2.5.1.81 (UniProt)
UniProt
Find proteins for Q8PYS1 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PYS1  Go to UniProtKB:  Q8PYS1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.251 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.16	α = 90
b = 81.273	β = 90
c = 49.689	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Kumaran, D., Mohammed, M.B., Brown, A., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2015-04-29
  Changes: Non-polymer description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary