3KIP | pdb_00003kip

Crystal structure of type-II 3-dehydroquinase from C. albicans

PDB DOI: https://doi.org/10.2210/pdb3KIP/pdb

Classification: LYASE
Organism(s): Candida albicans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-11-02 Released: 2010-05-12
Deposition Author(s): Trapani, S., Schoehn, G., Navaza, J., Abergel, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.245 (Depositor), 0.242 (DCC)
R-Value Work:
0.203 (Depositor)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions.

Trapani, S., Schoehn, G., Navaza, J., Abergel, C.

(2010) Acta Crystallogr D Biol Crystallogr 66: 514-521

PubMed: 20445226 Search on PubMed
DOI: https://doi.org/10.1107/S0907444910002763
Primary Citation Related Structures:
3KIP

PubMed Abstract:
The combination of transmission electron microscopy with X-ray diffraction data is usually limited to relatively large particles. Here, the approach is continued one step further by utilizing negative staining, a technique that is of wider applicability than cryo-electron microscopy, to produce models of medium-size proteins suitable for molecular replacement. The technique was used to solve the crystal structure of the dodecameric type II dehydroquinase enzyme from Candida albicans (approximately 190 kDa) and that of the orthologous Streptomyces coelicolor protein.

Organizational Affiliation

Université de Montpellier 1, Montpellier, France. stefano.trapani@cbs.cnrs.fr

Macromolecule Content

Total Structure Weight: 446.63 kDa
Atom Count: 27,144
Modeled Residue Count: 3,456
Deposited Residue Count: 4,008
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinase, type II	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	167	Candida albicans	Mutation(s): 0 Gene Names: DQD1, DHQ99, CaO19.9823 EC: 4.2.1.10
UniProt
Find proteins for Q59Z17 (Candida albicans (strain SC5314 / ATCC MYA-2876)) Explore Q59Z17 Go to UniProtKB: Q59Z17
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q59Z17
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain CB [auth W] SDF format, chain MA [auth J] SDF format, chain QA [auth N] SDF format, chain TA [auth P] SDF format, chain YA [auth T] SDF format, chain IA [auth G] SDF format, chain EA [auth D] SDF format, chain AA [auth A] MOL2 format, chain CB [auth W] MOL2 format, chain MA [auth J] MOL2 format, chain QA [auth N] MOL2 format, chain TA [auth P] MOL2 format, chain YA [auth T] MOL2 format, chain IA [auth G] MOL2 format, chain EA [auth D] MOL2 format, chain AA [auth A] mmCIF format, chain CB [auth W] mmCIF format, chain MA [auth J] mmCIF format, chain QA [auth N] mmCIF format, chain TA [auth P] mmCIF format, chain YA [auth T] mmCIF format, chain IA [auth G] mmCIF format, chain EA [auth D] mmCIF format, chain AA [auth A]	AA [auth A] CB [auth W] EA [auth D] IA [auth G] MA [auth J] AA [auth A], CB [auth W], EA [auth D], IA [auth G], MA [auth J], QA [auth N], TA [auth P], YA [auth T]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain AA [auth A] Focus chain CB [auth W] Focus chain EA [auth D] Focus chain IA [auth G] Focus chain MA [auth J] Focus chain QA [auth N] Focus chain TA [auth P] Focus chain YA [auth T] Interactions & Density Focus chain AA [auth A] Focus chain CB [auth W] Focus chain EA [auth D] Focus chain IA [auth G] Focus chain MA [auth J] Focus chain QA [auth N] Focus chain TA [auth P] Focus chain YA [auth T]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AB [auth V] SDF format, chain BB [auth W] SDF format, chain CA [auth C] SDF format, chain DA [auth D] SDF format, chain GA [auth F] SDF format, chain JA [auth H] SDF format, chain KA [auth I] SDF format, chain LA [auth J] SDF format, chain NA [auth K] SDF format, chain OA [auth M] SDF format, chain RA [auth O] SDF format, chain SA [auth P] SDF format, chain UA [auth Q] SDF format, chain VA [auth R] SDF format, chain Z [auth A] SDF format, chain ZA [auth U] SDF format, chain Y [auth A] SDF format, chain XA [auth T] SDF format, chain WA [auth S] SDF format, chain PA [auth N] SDF format, chain HA [auth G] SDF format, chain FA [auth E] SDF format, chain DB [auth X] SDF format, chain BA [auth B] MOL2 format, chain AB [auth V] MOL2 format, chain BB [auth W] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain GA [auth F] MOL2 format, chain JA [auth H] MOL2 format, chain KA [auth I] MOL2 format, chain LA [auth J] MOL2 format, chain NA [auth K] MOL2 format, chain OA [auth M] MOL2 format, chain RA [auth O] MOL2 format, chain SA [auth P] MOL2 format, chain UA [auth Q] MOL2 format, chain VA [auth R] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth U] MOL2 format, chain Y [auth A] MOL2 format, chain XA [auth T] MOL2 format, chain WA [auth S] MOL2 format, chain PA [auth N] MOL2 format, chain HA [auth G] MOL2 format, chain FA [auth E] MOL2 format, chain DB [auth X] MOL2 format, chain BA [auth B] mmCIF format, chain AB [auth V] mmCIF format, chain BB [auth W] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain GA [auth F] mmCIF format, chain JA [auth H] mmCIF format, chain KA [auth I] mmCIF format, chain LA [auth J] mmCIF format, chain NA [auth K] mmCIF format, chain OA [auth M] mmCIF format, chain RA [auth O] mmCIF format, chain SA [auth P] mmCIF format, chain UA [auth Q] mmCIF format, chain VA [auth R] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth U] mmCIF format, chain Y [auth A] mmCIF format, chain XA [auth T] mmCIF format, chain WA [auth S] mmCIF format, chain PA [auth N] mmCIF format, chain HA [auth G] mmCIF format, chain FA [auth E] mmCIF format, chain DB [auth X] mmCIF format, chain BA [auth B]	AB [auth V] BA [auth B] BB [auth W] CA [auth C] DA [auth D] AB [auth V], BA [auth B], BB [auth W], CA [auth C], DA [auth D], DB [auth X], FA [auth E], GA [auth F], HA [auth G], JA [auth H], KA [auth I], LA [auth J], NA [auth K], OA [auth M], PA [auth N], RA [auth O], SA [auth P], UA [auth Q], VA [auth R], WA [auth S], XA [auth T], Y [auth A], Z [auth A], ZA [auth U]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth V] Focus chain BA [auth B] Focus chain BB [auth W] Focus chain CA [auth C] Focus chain DA [auth D] Focus chain DB [auth X] Focus chain FA [auth E] Focus chain GA [auth F] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain KA [auth I] Focus chain LA [auth J] Focus chain NA [auth K] Focus chain OA [auth M] Focus chain PA [auth N] Focus chain RA [auth O] Focus chain SA [auth P] Focus chain UA [auth Q] Focus chain VA [auth R] Focus chain WA [auth S] Focus chain XA [auth T] Focus chain Y [auth A] Focus chain Z [auth A] Focus chain ZA [auth U] Interactions & Density Focus chain AB [auth V] Focus chain BA [auth B] Focus chain BB [auth W] Focus chain CA [auth C] Focus chain DA [auth D] Focus chain DB [auth X] Focus chain FA [auth E] Focus chain GA [auth F] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain KA [auth I] Focus chain LA [auth J] Focus chain NA [auth K] Focus chain OA [auth M] Focus chain PA [auth N] Focus chain RA [auth O] Focus chain SA [auth P] Focus chain UA [auth Q] Focus chain VA [auth R] Focus chain WA [auth S] Focus chain XA [auth T] Focus chain Y [auth A] Focus chain Z [auth A] Focus chain ZA [auth U]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.245 (Depositor), 0.242 (DCC)
R-Value Work: 0.203 (Depositor)
R-Value Observed: 0.205 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.103	α = 90
b = 308.11	β = 90
c = 97.152	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-05-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-05-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-03-21
Changes: Database references
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-04-03
Changes: Refinement description