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- PDB-4v40: BETA-GALACTOSIDASE -

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Basic information

Entry
Database: PDB / ID: 4v40
TitleBETA-GALACTOSIDASE
ComponentsBETA-GALACTOSIDASE
KeywordsHYDROLASE (O-GLYCOSYL)
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. / 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 / Galactose mutarotase-like domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsJacobson, R.H. / Zhang, X. / Dubose, R.F. / Matthews, B.W.
Citation
Journal: Nature / Year: 1994
Title: Three-dimensional structure of beta-galactosidase from E. coli.
Authors: Jacobson, R.H. / Zhang, X.J. / DuBose, R.F. / Matthews, B.W.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization of Beta-Galactosidase from Escherichia Coli
Authors: Jacobson, R.H. / Matthews, B.W.
History
DepositionJul 18, 1994Processing site: BNL
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1BGL, 1BGM
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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 / _struct_conn.ptnr2_label_seq_id

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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
E: BETA-GALACTOSIDASE
F: BETA-GALACTOSIDASE
G: BETA-GALACTOSIDASE
H: BETA-GALACTOSIDASE
I: BETA-GALACTOSIDASE
J: BETA-GALACTOSIDASE
K: BETA-GALACTOSIDASE
L: BETA-GALACTOSIDASE
M: BETA-GALACTOSIDASE
N: BETA-GALACTOSIDASE
O: BETA-GALACTOSIDASE
P: BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,864,29447
Polymers1,863,54116
Non-polymers75331
Water26,2121455
1
A: BETA-GALACTOSIDASE
B: BETA-GALACTOSIDASE
C: BETA-GALACTOSIDASE
D: BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,08012
Polymers465,8854
Non-polymers1948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: BETA-GALACTOSIDASE
F: BETA-GALACTOSIDASE
G: BETA-GALACTOSIDASE
H: BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,08012
Polymers465,8854
Non-polymers1948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: BETA-GALACTOSIDASE
J: BETA-GALACTOSIDASE
K: BETA-GALACTOSIDASE
L: BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,08012
Polymers465,8854
Non-polymers1948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: BETA-GALACTOSIDASE
N: BETA-GALACTOSIDASE
O: BETA-GALACTOSIDASE
P: BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,05511
Polymers465,8854
Non-polymers1707
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.900, 207.500, 509.900
Angle α, β, γ (deg.)90.00, 94.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BETA-GALACTOSIDASE /


Mass: 116471.297 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P00722, beta-galactosidase
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1455 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 60 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Mar 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRedundancy: 2.1 % / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
TNT5Drefinement
TNTV. 5-Drefinement
WEISdata reduction
RefinementResolution: 2.5→8 Å / σ(F): 0 /
RfactorNum. reflection
obs0.174 537372
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms131072 0 0 1582 132654
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg2.5
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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