4MM2 | pdb_00004mm2

Crystal structure of yeast primase catalytic subunit

PDB DOI: https://doi.org/10.2210/pdb4MM2/pdb

Classification: REPLICATION
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-09-07 Released: 2014-09-10
Deposition Author(s): Park, K.R., An, J.Y., Lee, Y., Youn, H.S., Lee, J.G., Kang, J.Y., Kim, T.G., Lim, J.J., Eom, S.H., Wang, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.293 (Depositor), 0.298 (DCC)
R-Value Work:
0.255 (Depositor), 0.268 (DCC)
R-Value Observed:
0.257 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of yeast primase catalytic subunit

Park, K.R., An, J.Y., Lee, Y., Youn, H.S., Lee, J.G., Kang, J.Y., Kim, T.G., Lim, J.J., Eom, S.H., Wang, J.

To be published.

Macromolecule Content

Total Structure Weight: 97.84 kDa
Atom Count: 6,980
Modeled Residue Count: 790
Deposited Residue Count: 828
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA primase small subunit	A, B	414	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: PRI1, YIR008C, YIB8C EC: 2.7.7
UniProt
Find proteins for P10363 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P10363 Go to UniProtKB: P10363
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10363
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B]	H [auth A], N [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.293 (Depositor), 0.298 (DCC)
R-Value Work: 0.255 (Depositor), 0.268 (DCC)
R-Value Observed: 0.257 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.37	α = 90
b = 196.04	β = 114.72
c = 53.96	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-09-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-10
Type: Initial release
Version 1.1: 2019-12-04
Changes: Data collection, Database references, Refinement description
Version 1.2: 2019-12-18
Changes: Data collection
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description