3RJL

Crystal structure of 1-pyrroline-5-carboxylate dehydrogenase from Bacillus licheniformis (Target NYSGRC-000337)

PDB DOI: https://doi.org/10.2210/pdb3RJL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bacillus licheniformis DSM 13 = ATCC 14580
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-04-15 Released: 2011-04-27
Deposition Author(s): Patskovsky, Y., Toro, R., Foti, R., Seidel, R.D., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.292
R-Value Work: 0.222
R-Value Observed: 0.224

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of 1-Pyrroline-5-Carboxylate Dehydrogenase from Bacillus Licheniformis

Patskovsky, Y., Toro, R., Foti, R., Seidel, R.D., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 482.13 kDa
Atom Count: 32,569
Modelled Residue Count: 4,105
Deposited Residue Count: 4,304
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-pyrroline-5-carboxylate dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	538	Bacillus licheniformis DSM 13 = ATCC 14580	Mutation(s): 0 Gene Names: rocA, BLi00374, BL01710 EC: 1.5.1.12 (PDB Primary Data), 1.2.1.88 (UniProt)
UniProt
Find proteins for Q65NN2 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65NN2 Go to UniProtKB: Q65NN2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q65NN2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain BB [auth G] SDF format, chain CA [auth C] SDF format, chain CB [auth G] SDF format, chain DA [auth C] SDF format, chain DB [auth G] SDF format, chain EA [auth C] SDF format, chain EB [auth G] SDF format, chain FA [auth C] SDF format, chain FB [auth G] SDF format, chain GA [auth C] SDF format, chain GB [auth G] SDF format, chain HA [auth C] SDF format, chain HB [auth H] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain IB [auth H] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain JB [auth H] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain Q [auth A] SDF format, chain QA [auth E] SDF format, chain RA [auth E] SDF format, chain S [auth B] SDF format, chain SA [auth E] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain VA [auth F] SDF format, chain WA [auth F] SDF format, chain X [auth C] SDF format, chain XA [auth F] SDF format, chain Y [auth C] SDF format, chain YA [auth F] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth G] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth G] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth G] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth G] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth G] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth G] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth H] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain IB [auth H] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain JB [auth H] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain WA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth G] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth G] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth G] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth G] mmCIF format, chain FA [auth C] mmCIF format, chain FB [auth G] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth G] mmCIF format, chain HA [auth C] mmCIF format, chain HB [auth H] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain IB [auth H] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain JB [auth H] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth E] mmCIF format, chain RA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain WA [auth F] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth F] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth F] mmCIF format, chain Z [auth C]	AA [auth C] BA [auth C] BB [auth G] CA [auth C] CB [auth G] AA [auth C], BA [auth C], BB [auth G], CA [auth C], CB [auth G], DA [auth C], DB [auth G], EA [auth C], EB [auth G], FA [auth C], FB [auth G], GA [auth C], GB [auth G], HA [auth C], HB [auth H], I [auth A], IA [auth D], IB [auth H], J [auth A], JA [auth D], JB [auth H], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], O [auth A], OA [auth E], P [auth A], PA [auth E], Q [auth A], QA [auth E], RA [auth E], S [auth B], SA [auth E], T [auth B], U [auth B], V [auth B], VA [auth F], WA [auth F], X [auth C], XA [auth F], Y [auth C], YA [auth F], Z [auth C]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain BB [auth G] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain DA [auth C] Focus chain DB [auth G] Focus chain EA [auth C] Focus chain EB [auth G] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain GB [auth G] Focus chain HA [auth C] Focus chain HB [auth H] Focus chain I [auth A] Focus chain IA [auth D] Focus chain IB [auth H] Focus chain J [auth A] Focus chain JA [auth D] Focus chain JB [auth H] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain X [auth C] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain BB [auth G] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain DA [auth C] Focus chain DB [auth G] Focus chain EA [auth C] Focus chain EB [auth G] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain GB [auth G] Focus chain HA [auth C] Focus chain HB [auth H] Focus chain I [auth A] Focus chain IA [auth D] Focus chain IB [auth H] Focus chain J [auth A] Focus chain JA [auth D] Focus chain JB [auth H] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Focus chain X [auth C] Focus chain XA [auth F] Focus chain Y [auth C] Focus chain YA [auth F] Focus chain Z [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain KB [auth H] SDF format, chain NA [auth D] SDF format, chain R [auth A] SDF format, chain TA [auth E] SDF format, chain UA [auth E] SDF format, chain W [auth B] SDF format, chain ZA [auth F] MOL2 format, chain AB [auth F] MOL2 format, chain KB [auth H] MOL2 format, chain NA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain TA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain ZA [auth F] mmCIF format, chain AB [auth F] mmCIF format, chain KB [auth H] mmCIF format, chain NA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain TA [auth E] mmCIF format, chain UA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain ZA [auth F]	AB [auth F] KB [auth H] NA [auth D] R [auth A] TA [auth E] AB [auth F], KB [auth H], NA [auth D], R [auth A], TA [auth E], UA [auth E], W [auth B], ZA [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AB [auth F] Focus chain KB [auth H] Focus chain NA [auth D] Focus chain R [auth A] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain W [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth F] Focus chain KB [auth H] Focus chain NA [auth D] Focus chain R [auth A] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain W [auth B] Focus chain ZA [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.292
R-Value Work: 0.222
R-Value Observed: 0.224
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.267	α = 90
b = 116.114	β = 90.15
c = 181.768	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-04-27

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2011-04-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description