3CR7 | pdb_00003cr7

Crystal structure of N-terminal truncation of APS Kinase from Penicillium chrysogenum: Ternary structure with ADP and PAPS

PDB DOI: https://doi.org/10.2210/pdb3CR7/pdb

Classification: TRANSFERASE
Organism(s): Penicillium chrysogenum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-04-04 Released: 2009-02-17
Deposition Author(s): Gay, S.C., Segel, I.H., Fisher, A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.279 (Depositor), 0.266 (DCC)
R-Value Work:
0.198 (Depositor), 0.240 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Truncated APS kinase from Pencillium chrysogenum: Insight into the function of the N-terminal helix

Gay, S.C., Segel, I.H., Fisher, A.J.

To be published.

Macromolecule Content

Total Structure Weight: 92.25 kDa
Atom Count: 6,230
Modeled Residue Count: 721
Deposited Residue Count: 788
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylyl-sulfate kinase	A, B, C, D	197	Penicillium chrysogenum	Mutation(s): 0 EC: 2.7.1.25
UniProt
Find proteins for Q12657 (Penicillium chrysogenum) Explore Q12657 Go to UniProtKB: Q12657
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12657
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PPS Query on PPS Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain G [auth A] MOL2 format, chain L [auth C] MOL2 format, chain G [auth A] mmCIF format, chain L [auth C] mmCIF format, chain G [auth A]	G [auth A], L [auth C]	3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE C₁₀ H₁₅ N₅ O₁₃ P₂ S GACDQMDRPRGCTN-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain L [auth C] Interactions & Density Focus chain G [auth A] Focus chain L [auth C]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	F [auth A], I [auth B], K [auth C], M [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], J [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.279 (Depositor), 0.266 (DCC)
R-Value Work: 0.198 (Depositor), 0.240 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.58	α = 90
b = 82.594	β = 90
c = 139.009	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
EPMR	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-02-17

Deposition Author(s):

Gay, S.C.

Segel, I.H.

Fisher, A.J.

Revision History (Full details and data files)

Version 1.0: 2009-02-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

3CR7 | pdb_00003cr7

Crystal structure of N-terminal truncation of APS Kinase from Penicillium chrysogenum: Ternary structure with ADP and PAPS

Literature

Truncated APS kinase from Pencillium chrysogenum: Insight into the function of the N-terminal helix

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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