3NAI | pdb_00003nai

Crystal structures and functional analysis of murine norovirus RNA-dependent RNA polymerase

PDB DOI: https://doi.org/10.2210/pdb3NAI/pdb

Classification: TRANSFERASE
Organism(s): Murine norovirus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-06-02 Released: 2011-06-08
Deposition Author(s): Kim, K.H., Lee, J.H., Alam, I., Park, Y., Kang, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free:
0.268 (Depositor), 0.269 (DCC)
R-Value Work:
0.203 (Depositor), 0.203 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structures and functional analysis of murine norovirus RNA-dependent RNA polymerase

Kim, K.H., Lee, J.H., Alam, I., Park, Y., Kang, S.

To be published.

Macromolecule Content

Total Structure Weight: 177.88 kDa
Atom Count: 12,037
Modeled Residue Count: 1,458
Deposited Residue Count: 1,551
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA dependent RNA polymerase	A, B, C	517	Murine norovirus 1	Mutation(s): 0
UniProt
Find proteins for Q80J95 (Norovirus (isolate Mouse/NoV/United States/MNV1/2002/GV)) Explore Q80J95 Go to UniProtKB: Q80J95
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q80J95
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
URF Query on URF Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain P [auth B] SDF format, chain E [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain P [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Y [auth C] mmCIF format, chain P [auth B] mmCIF format, chain E [auth A]	E [auth A], P [auth B], Y [auth C]	5-FLUOROURACIL C₄ H₃ F N₂ O₂ GHASVSINZRGABV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain P [auth B] Focus chain Y [auth C] Interactions & Density Focus chain E [auth A] Focus chain P [auth B] Focus chain Y [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain U [auth B] SDF format, chain K [auth A] SDF format, chain H [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain U [auth B] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain U [auth B] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A]	BA [auth C] CA [auth C] DA [auth C] H [auth A] I [auth A] BA [auth C], CA [auth C], DA [auth C], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain N [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain N [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain N [auth A]	EA [auth C], N [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain N [auth A] Interactions & Density Focus chain EA [auth C] Focus chain N [auth A]
MN3 Query on MN3 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Z [auth C]	AA [auth C] F [auth A] G [auth A] Q [auth B] R [auth B] AA [auth C], F [auth A], G [auth A], Q [auth B], R [auth B], Z [auth C]	MANGANESE (III) ION Mn MMIPFLVOWGHZQD-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Z [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain X [auth C] SDF format, chain D [auth A] MOL2 format, chain O [auth B] MOL2 format, chain X [auth C] MOL2 format, chain D [auth A] mmCIF format, chain O [auth B] mmCIF format, chain X [auth C] mmCIF format, chain D [auth A]	D [auth A], O [auth B], X [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain O [auth B] Focus chain X [auth C] Interactions & Density Focus chain D [auth A] Focus chain O [auth B] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free: 0.268 (Depositor), 0.269 (DCC)
R-Value Work: 0.203 (Depositor), 0.203 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.246	α = 90
b = 196.562	β = 114.81
c = 109.598	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-06-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-06-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-03-20
Changes: Data collection, Database references, Derived calculations