3MV0 | pdb_00003mv0

E. COLI (lacZ) BETA-GALACTOSIDASE (R599A) IN COMPLEX WITH D-GALCTOPYRANOSYL-1-ONE

• PDB DOI: https://doi.org/10.2210/pdb3MV0/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-05-03 Released: 2011-03-16 
• Deposition Author(s): Dugdale, M.L., Vance, M., Driedger, M.L., Nibber, A., Tran, A., Huber, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.237 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.192 (DCC) 

Starting Model: experimental

Literature

Importance of Arg-599 of b-galactosidase (Escherichia coli) as an anchor for the open conformations of Phe-601 and the active-site loop

Dugdale, M.L., Vance, M.L., Wheatley, R.W., Driedger, M.R., Nibber, A., Tran, A., Huber, R.E.

(2010) Biochem Cell Biol 88: 969-979

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 489.51 kDa 
• Atom Count: 36,190 
• Modeled Residue Count: 4,044 
• Deposited Residue Count: 4,208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A [auth 1], B [auth 2], C [auth 3], D [auth 4]	1,052	Escherichia coli K-12	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
149	BC [auth 3], E [auth 1], NA [auth 2], QD [auth 4]	D-galactonolactone C6 H10 O6 PHOQVHQSTUBQQK-MGCNEYSASA-N
DMS	AA [auth 1], AB [auth 2], AC [auth 3], AD [auth 3], AE [auth 4], AF [auth 4], BA [auth 1], BB [auth 2], BD [auth 3], BE [auth 4], CA [auth 1], CB [auth 2], CD [auth 3], CE [auth 4], DA [auth 1], DB [auth 2], DD [auth 3], DE [auth 4], EA [auth 1], EB [auth 2], ED [auth 3], EE [auth 4], FA [auth 1], FB [auth 2], FD [auth 3], FE [auth 4], GA [auth 1], GB [auth 2], GD [auth 3], GE [auth 4], HA [auth 1], HB [auth 2], HD [auth 3], HE [auth 4], IA [auth 1], IB [auth 2], ID [auth 3], IE [auth 4], JA [auth 1], JB [auth 2], JC [auth 3], JD [auth 3], JE [auth 4], KA [auth 1], KB [auth 2], KC [auth 3], KD [auth 3], KE [auth 4], L [auth 1], LA [auth 1], LB [auth 2], LC [auth 3], LD [auth 3], LE [auth 4], M [auth 1], MA [auth 1], MB [auth 2], MC [auth 3], MD [auth 3], ME [auth 4], N [auth 1], NB [auth 2], NC [auth 3], ND [auth 3], NE [auth 4], O [auth 1], OB [auth 2], OC [auth 3], OD [auth 3], OE [auth 4], P [auth 1], PB [auth 2], PC [auth 3], PD [auth 3], PE [auth 4], Q [auth 1], QB [auth 2], QC [auth 3], QE [auth 4], R [auth 1], RB [auth 2], RC [auth 3], RE [auth 4], S [auth 1], SB [auth 2], SC [auth 3], SE [auth 4], T [auth 1], TB [auth 2], TC [auth 3], TE [auth 4], U [auth 1], UB [auth 2], UC [auth 3], UE [auth 4], V [auth 1], VA [auth 2], VB [auth 2], VC [auth 3], VE [auth 4], W [auth 1], WA [auth 2], WB [auth 2], WC [auth 3], WE [auth 4], X [auth 1], XA [auth 2], XB [auth 2], XC [auth 3], XE [auth 4], Y [auth 1], YA [auth 2], YB [auth 2], YC [auth 3], YD [auth 4], YE [auth 4], Z [auth 1], ZA [auth 2], ZB [auth 2], ZC [auth 3], ZD [auth 4], ZE [auth 4]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	CC [auth 3], DC [auth 3], EC [auth 3], F [auth 1], G [auth 1], OA [auth 2], PA [auth 2], QA [auth 2], RD [auth 4], SD [auth 4], TD [auth 4]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	FC [auth 3], GC [auth 3], H [auth 1], HC [auth 3], I [auth 1], IC [auth 3], J [auth 1], K [auth 1], RA [auth 2], SA [auth 2], TA [auth 2], UA [auth 2], UD [auth 4], VD [auth 4], WD [auth 4], XD [auth 4]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.237 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.192 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.84	α = 90
b = 166.31	β = 90
c = 201.71	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-16 
Deposition Author(s): Dugdale, M.L., Vance, M., Driedger, M.L., Nibber, A., Tran, A., Huber, R.E.

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description