2QDD | pdb_00002qdd

Crystal structure of a member of enolase superfamily from Roseovarius nubinhibens ISM

PDB DOI: https://doi.org/10.2210/pdb2QDD/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Roseovarius nubinhibens ISM
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-06-20 Released: 2007-06-26
Deposition Author(s): Patskovsky, Y., Bonanno, J., Sauder, J.M., Gilmore, J.M., Iizuka, M., Groshong, C., Gheyi, T., Sojitra, S., Wasserman, S.R., Koss, J., Gerlt, J., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.228 (Depositor), 0.226 (DCC)
R-Value Work:
0.182 (Depositor), 0.178 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of a member of enolase superfamily from Roseovarius nubinhibens ISM.

Patskovsky, Y., Bonanno, J., Sauder, J.M., Gilmore, J.M., Iizuka, M., Groshong, C., Gheyi, T., Sojitra, S., Wasserman, S.R., Koss, J., Gerlt, J., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 81.54 kDa
Atom Count: 5,975
Modeled Residue Count: 736
Deposited Residue Count: 756
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme	A, B	378	Roseovarius nubinhibens ISM	Mutation(s): 0 Gene Names: COG4948, ISM_14065
UniProt
Find proteins for A3SNF7 (Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM)) Explore A3SNF7 Go to UniProtKB: A3SNF7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3SNF7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.228 (Depositor), 0.226 (DCC)
R-Value Work: 0.182 (Depositor), 0.178 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.842	α = 90
b = 126.842	β = 90
c = 96.608	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-06-26

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-06-26
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-11-14
Changes: Data collection, Structure summary
Version 1.5: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.6: 2024-02-21
Changes: Data collection, Database references, Refinement description