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- PDB-3czj: E. COLI (lacZ) BETA-GALACTOSIDASE (N460T) IN COMPLEX WITH D-GALCT... -

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Basic information

Entry
Database: PDB / ID: 3czj
TitleE. COLI (lacZ) BETA-GALACTOSIDASE (N460T) IN COMPLEX WITH D-GALCTOPYRANOSYL-1-ONE
ComponentsBeta-galactosidase
KeywordsHYDROLASE / Asn-460-Thr BETA-GALACTOSIDASE HYDROLASE TIM BARREL (ALPHA/BETA BARREL) JELLY-ROLL BARREL IMMUNOGLOBULIN BETA SUPERSANDWICH / Glycosidase
Function / homology
Function and homology information


alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding
Similarity search - Function
Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. ...Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Distorted Sandwich / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
D-galactonolactone / Beta-galactosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHuber, R.E. / Dugdale, M.L. / Fraser, M.E. / Tammam, S.D.
CitationJournal: Protein J. / Year: 2009
Title: Practical Considerations When Using Temperature to Obtain Rate Constants and Activation Thermodynamics of Enzymes with Two Catalytic Steps: Native and N460T-beta-Galactosidase (E. coli) as Examples.
Authors: Kappelhoff, J.C. / Liu, S.Y. / Dugdale, M.L. / Dymianiw, D.L. / Linton, L.R. / Huber, R.E.
History
DepositionApr 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 5, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Jul 29, 2020Group: Derived calculations
Category: pdbx_struct_conn_angle / struct_conn ...pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,617127
Polymers465,9734
Non-polymers8,644123
Water46,9652607
1
A: Beta-galactosidase
B: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,85194
Polymers349,4803
Non-polymers6,37291
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16050 Å2
ΔGint0 kcal/mol
Surface area73400 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14210 Å2
ΔGint-22 kcal/mol
Surface area72830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.443, 161.643, 202.155
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Beta-galactosidase / / Lactase


Mass: 116493.266 Da / Num. of mol.: 4 / Mutation: N461T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lacZ, b0344, JW0335 / Plasmid: pBAD/HIS/LACZ / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: P00722, beta-galactosidase
#2: Sugar
ChemComp-149 / D-galactonolactone / (3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-one


Type: D-saccharide / Mass: 178.140 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H10O6

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Non-polymers , 4 types, 2726 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Na
#5: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 94 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2607 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, NaCl, MgCl2, DTT, Bis-Tris, pH 6.5, HANGING DROP at 288K, pH 6.50, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 25, 2006 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.05→75.05 Å / Num. all: 249249 / Num. obs: 249249 / % possible obs: 81.1 % / Observed criterion σ(F): 0 / Redundancy: 2.06 % / Biso Wilson estimate: 10.6 Å2 / Limit h max: 73 / Limit h min: 0 / Limit k max: 59 / Limit k min: 0 / Limit l max: 92 / Limit l min: 0 / Observed criterion F max: 6262287.43 / Observed criterion F min: 9.827
Reflection shellHighest resolution: 2.05 Å / Redundancy: 2.06 % / Mean I/σ(I) obs: 13 / Num. unique all: 308903 / % possible all: 81.1

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DPO

1dpo


Resolution: 2.05→75.05 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Cross-validation method: -> "throughout" Free R value test set selection criteria: -> "random" Number of non-hydrogen atoms used in refinement. Polymer 32496 Nonpolymer 1106 Solvent 2072 CNS ...Details: Cross-validation method: -> "throughout" Free R value test set selection criteria: -> "random" Number of non-hydrogen atoms used in refinement. Polymer 32496 Nonpolymer 1106 Solvent 2072 CNS Parameter files: CNS_TOPPAR/protein_rep.param CNS_TOPPAR/water.param CNS_TOPPAR/ion.param ../dms_xplor_par.txt ../149_xplor_par.txt CNS Topology files: CNS_TOPPAR/protein.top CNS_TOPPAR/water.top CNS_TOPPAR/ion.top ../dms_xplor_top.txt ../149_xplor_top.txt
RfactorNum. reflection% reflectionSelection details
Rfree0.231 3564 1.4 %1.5%, consistent with previous structures.
Rwork0.193 ---
all0.194 308903 --
obs0.194 249249 80.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 55.9575 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 108.16 Å2 / Biso mean: 18.43 Å2 / Biso min: 1.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2--1.6 Å20 Å2
3----1.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.11 Å
Luzzati d res high-2.05
Refinement stepCycle: LAST / Resolution: 2.05→75.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32496 0 449 2607 35552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg25.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.91
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.05-2.140.2882781.50.213186180.017383551889649.3
2.14-2.260.2643681.40.198259270.014383712629568.5
2.26-2.40.2494181.50.193277890.012384212820773.4
2.4-2.580.2374611.50.187297100.011384693017178.4
2.58-2.840.2414531.40.192321120.011385273256584.5
2.84-3.250.2355081.40.192350990.01386153560792.2
3.25-4.10.2145441.40.183378990.009388123844399
4.1-75.050.2115341.40.199385310.009396133906598.6

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