3AF5

The crystal structure of an archaeal CPSF subunit, PH1404 from Pyrococcus horikoshii

PDB DOI: https://doi.org/10.2210/pdb3AF5/pdb

Classification: HYDROLASE
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-02-23 Released: 2010-04-21
Deposition Author(s): Nishida, Y., Ishikawa, H., Nakagawa, N., Masui, R., Kuramitsu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.237 (Depositor), 0.230 (DCC)
R-Value Work:
0.196 (Depositor), 0.190 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii

Nishida, Y., Ishikawa, H., Baba, S., Nakagawa, N., Kuramitsu, S., Masui, R.

(2010) Proteins 78: 2395-2398

PubMed: 20544974 Search on PubMed
DOI: https://doi.org/10.1002/prot.22748
Primary Citation of Related Structures:
3AF5, 3AF6

Organizational Affiliation

Graduate School of Frontier Biological Sciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.

Macromolecule Content

Total Structure Weight: 75.13 kDa
Atom Count: 5,218
Modelled Residue Count: 638
Deposited Residue Count: 651
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein PH1404	A	651	Pyrococcus horikoshii OT3	Mutation(s): 0 Gene Names: PH1404 EC: 3.1
UniProt
Find proteins for O50112 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O50112 Go to UniProtKB: O50112
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O50112
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] 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] Interactions & Density Focus chain B [auth A] 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]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A]	L [auth A], M [auth A], N [auth A], O [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	H [auth A], I [auth A], J [auth A], K [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.237 (Depositor), 0.230 (DCC)
R-Value Work: 0.196 (Depositor), 0.190 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.2	α = 90
b = 86.2	β = 90
c = 238.287	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-04-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-04-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations