3VD9
E. coli (lacZ) beta-galactosidase (N460S) in complex with IPTG
- PDB DOI: https://doi.org/10.2210/pdb3VD9/pdb
- Classification: HYDROLASE
- Organism(s): Escherichia coli
- Expression System: Escherichia coli
- Mutation(s): Yes 
- Deposited: 2012-01-04 Released: 2012-04-11 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 Å
- R-Value Free: 0.223 
- R-Value Work: 0.169 
- R-Value Observed: 0.170 
This is version 1.4 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Beta-galactosidase | 1,052 | Escherichia coli | Mutation(s): 1  Gene Names: lacZ EC: 3.2.1.23 | ||
UniProt | |||||
Find proteins for P00722 (Escherichia coli (strain K12)) Explore P00722  Go to UniProtKB:  P00722 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00722 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
IPT Query on IPT | EC [auth D], GA [auth B], HB [auth C], K [auth A] | 1-methylethyl 1-thio-beta-D-galactopyranoside C9 H18 O5 S BPHPUYQFMNQIOC-NXRLNHOXSA-N | |||
DMS Query on DMS | AB [auth B] FC [auth D] GC [auth D] HA [auth B] HC [auth D] | DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N | |||
MG Query on MG | AA [auth B] AC [auth D] BB [auth C] CB [auth C] E [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N | |||
NA Query on NA | BA [auth B] BC [auth D] CA [auth B] CC [auth D] DA [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 Å
- R-Value Free: 0.223 
- R-Value Work: 0.169 
- R-Value Observed: 0.170 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 151.537 | α = 90 |
b = 162.55 | β = 90 |
c = 203.44 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
CNS | refinement |
ADSC | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2012-04-11  Deposition Author(s): Wheatley, R.W., Kappelhoff, J.C., Hahn, J.N., Dugdale, M.L., Dutkoski, M.J., Tamman, S.D., Fraser, M.E., Huber, R.E.
Revision History (Full details and data files)
- Version 1.0: 2012-04-11
Type: Initial release - Version 1.1: 2013-06-19
Changes: Database references - Version 1.2: 2019-07-17
Changes: Data collection, Refinement description - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.4: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary