4XQ2 | pdb_00004xq2

Ensemble refinement of cystathione gamma lyase (CalE6) D7G from Micromonospora echinospora

PDB DOI: https://doi.org/10.2210/pdb4XQ2/pdb

Classification: LYASE
Organism(s): Micromonospora echinospora
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-01-18 Released: 2015-04-15
Deposition Author(s): Wang, F., Yennamalli, R.M., Singh, S., Tan, K., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.183 (Depositor), 0.219 (DCC)
R-Value Work:
0.143 (Depositor), 0.181 (DCC)
R-Value Observed:
0.145 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

The crystal structure of cystathione gamma lyase (CalE6) from Micromonospora echinospora

Yennamalli, R.M., Tan, K., Wang, F., Bigelow, L., Jedrzejczak, R., Babnigg, G., Bingman, C.A., Joachimiak, A., Kharel, M.K., Singh, S., Thorson, J.S., Phillips Jr., G.N.

To be published.

Macromolecule Content

Total Structure Weight: 335.2 kDa
Atom Count: 24,344
Modeled Residue Count: 3,018
Deposited Residue Count: 3,072
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CalE6	A, B, C, D, E A, B, C, D, E, F, G, H	384	Micromonospora echinospora	Mutation(s): 1 Gene Names: calE6 EC: 4.4.1.2
UniProt
Find proteins for Q8KNG3 (Micromonospora echinospora) Explore Q8KNG3 Go to UniProtKB: Q8KNG3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8KNG3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain VA [auth G] SDF format, chain O [auth B] SDF format, chain MA [auth F] SDF format, chain IA [auth E] SDF format, chain I [auth A] SDF format, chain CB [auth H] SDF format, chain CA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain VA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain MA [auth F] MOL2 format, chain IA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain CB [auth H] MOL2 format, chain CA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain VA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain MA [auth F] mmCIF format, chain IA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain CB [auth H] mmCIF format, chain CA [auth D]	CA [auth D] CB [auth H] I [auth A] IA [auth E] MA [auth F] CA [auth D], CB [auth H], I [auth A], IA [auth E], MA [auth F], O [auth B], VA [auth G], X [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain CB [auth H] Focus chain I [auth A] Focus chain IA [auth E] Focus chain MA [auth F] Focus chain O [auth B] Focus chain VA [auth G] Focus chain X [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain ZA [auth G] SDF format, chain YA [auth G] SDF format, chain Y [auth C] SDF format, chain XA [auth G] SDF format, chain WA [auth G] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain SA [auth F] SDF format, chain S [auth B] SDF format, chain RA [auth F] SDF format, chain R [auth B] SDF format, chain QA [auth F] SDF format, chain Q [auth B] SDF format, chain PA [auth F] SDF format, chain P [auth B] SDF format, chain OA [auth F] SDF format, chain NA [auth F] SDF format, chain L [auth A] SDF format, chain KA [auth E] SDF format, chain K [auth A] SDF format, chain JA [auth E] SDF format, chain J [auth A] SDF format, chain FA [auth D] SDF format, chain EB [auth H] SDF format, chain EA [auth D] SDF format, chain DB [auth H] SDF format, chain DA [auth D] MOL2 format, chain ZA [auth G] MOL2 format, chain YA [auth G] MOL2 format, chain Y [auth C] MOL2 format, chain XA [auth G] MOL2 format, chain WA [auth G] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain NA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain EB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain DB [auth H] MOL2 format, chain DA [auth D] mmCIF format, chain ZA [auth G] mmCIF format, chain YA [auth G] mmCIF format, chain Y [auth C] mmCIF format, chain XA [auth G] mmCIF format, chain WA [auth G] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain SA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth F] mmCIF format, chain NA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain EB [auth H] mmCIF format, chain EA [auth D] mmCIF format, chain DB [auth H] mmCIF format, chain DA [auth D]	DA [auth D] DB [auth H] EA [auth D] EB [auth H] FA [auth D] DA [auth D], DB [auth H], EA [auth D], EB [auth H], FA [auth D], J [auth A], JA [auth E], K [auth A], KA [auth E], L [auth A], NA [auth F], OA [auth F], P [auth B], PA [auth F], Q [auth B], QA [auth F], R [auth B], RA [auth F], S [auth B], SA [auth F], T [auth B], U [auth B], V [auth B], WA [auth G], XA [auth G], Y [auth C], YA [auth G], ZA [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain EB [auth H] Focus chain FA [auth D] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain KA [auth E] Focus chain L [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain P [auth B] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain YA [auth G] Focus chain ZA [auth G]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain TA [auth F] SDF format, chain AB [auth G] MOL2 format, chain Z [auth C] MOL2 format, chain TA [auth F] MOL2 format, chain AB [auth G] mmCIF format, chain Z [auth C] mmCIF format, chain TA [auth F] mmCIF format, chain AB [auth G]	AB [auth G], TA [auth F], Z [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain TA [auth F] Focus chain Z [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain UA [auth F] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain LA [auth E] SDF format, chain HA [auth D] SDF format, chain GB [auth H] SDF format, chain GA [auth D] SDF format, chain FB [auth H] SDF format, chain BB [auth G] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain HA [auth D] MOL2 format, chain GB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain FB [auth H] MOL2 format, chain BB [auth G] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain HA [auth D] mmCIF format, chain GB [auth H] mmCIF format, chain GA [auth D] mmCIF format, chain FB [auth H] mmCIF format, chain BB [auth G] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] BB [auth G] FB [auth H] GA [auth D] AA [auth C], BA [auth C], BB [auth G], FB [auth H], GA [auth D], GB [auth H], HA [auth D], LA [auth E], M [auth A], N [auth A], UA [auth F], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain BB [auth G] Focus chain FB [auth H] Focus chain GA [auth D] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain LA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain UA [auth F] Focus chain W [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS
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: 2.10 Å
R-Value Free: 0.183 (Depositor), 0.219 (DCC)
R-Value Work: 0.143 (Depositor), 0.181 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.855	α = 90
b = 146.981	β = 90
c = 349.905	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-04-15

Deposition Author(s):

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Revision History (Full details and data files)

Version 1.0: 2015-04-15
Type: Initial release
Version 2.0: 2025-04-02
Changes: Advisory, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary