2OZ3 | pdb_00002oz3

Crystal structure of L-Rhamnonate dehydratase from Azotobacter vinelandii

PDB DOI: https://doi.org/10.2210/pdb2OZ3/pdb

Classification: LYASE
Organism(s): Azotobacter vinelandii DJ
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-02-23 Released: 2007-03-06
Deposition Author(s): Patskovsky, Y., Toro, R., Sauder, J.M., Freeman, J.C., Bain, K., Gheyi, T., Wu, B., Wasserman, S.R., Smith, D., 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: 2.00 Å
R-Value Free:
0.257 (Depositor), 0.257 (DCC)
R-Value Work:
0.196 (Depositor), 0.197 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.8 of the entry. See complete history.

Literature

Crystal structure of L-Rhamnonate dehydratase from azotobacter vinelandii

Patskovsky, Y., Toro, R., Sauder, J.M., Freeman, J.C., Bain, K., Wu, B., Gheyi, T., Wasserman, S.R., Smith, D., Gerlt, J., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 372.25 kDa
Atom Count: 26,576
Modeled Residue Count: 3,136
Deposited Residue Count: 3,232
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme	A, B, C, D, E A, B, C, D, E, F, G, H	404	Azotobacter vinelandii DJ	Mutation(s): 15 Gene Names: AVIN02004392, AvinDRAFT_6446 EC: 4.2.1.90
UniProt
Find proteins for C1DMY1 (Azotobacter vinelandii (strain DJ / ATCC BAA-1303)) Explore C1DMY1 Go to UniProtKB: C1DMY1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C1DMY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain OA [auth H] SDF format, chain O [auth A] SDF format, chain NA [auth H] SDF format, chain N [auth A] SDF format, chain MA [auth H] SDF format, chain M [auth A] SDF format, chain LA [auth G] SDF format, chain L [auth A] SDF format, chain KA [auth G] SDF format, chain K [auth A] SDF format, chain JA [auth F] SDF format, chain J [auth A] SDF format, chain IA [auth F] SDF format, chain I [auth A] SDF format, chain HA [auth E] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain EA [auth D] SDF format, chain DA [auth D] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth H] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth E] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] DA [auth D] EA [auth D] FA [auth D] AA [auth C], BA [auth C], DA [auth D], EA [auth D], FA [auth D], GA [auth D], HA [auth E], I [auth A], IA [auth F], J [auth A], JA [auth F], K [auth A], KA [auth G], L [auth A], LA [auth G], M [auth A], MA [auth H], N [auth A], NA [auth H], O [auth A], OA [auth H], P [auth A], Q [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth C], X [auth C], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth G] Focus chain L [auth A] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth H] Focus chain N [auth A] Focus chain NA [auth H] Focus chain O [auth A] Focus chain OA [auth H] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth G] Focus chain L [auth A] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth H] Focus chain N [auth A] Focus chain NA [auth H] Focus chain O [auth A] Focus chain OA [auth H] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain CA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain CA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain CA [auth D]	CA [auth D], R [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain R [auth B] Interactions & Density Focus chain CA [auth D] Focus chain R [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.257 (Depositor), 0.257 (DCC)
R-Value Work: 0.196 (Depositor), 0.197 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.772	α = 90
b = 115.397	β = 96.06
c = 164.113	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-03-06

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-03-06
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-18
Changes: Advisory, 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: 2023-08-30
Changes: Advisory, Data collection, Database references, Refinement description
Version 1.7: 2023-11-15
Changes: Data collection
Version 1.8: 2024-11-06
Changes: Structure summary