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- PDB-4v41: E. COLI (LAC Z) BETA-GALACTOSIDASE (NCS CONSTRAINED MONOMER-MONOC... -

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Basic information

Entry
Database: PDB / ID: 4v41
TitleE. COLI (LAC Z) BETA-GALACTOSIDASE (NCS CONSTRAINED MONOMER-MONOCLINIC)
ComponentsBETA-GALACTOSIDASE
KeywordsHYDROLASE / alpha/beta barrel / jelly roll barrel / fibronectin / beta supersandwich
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 ...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 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / 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
AuthorsJuers, D.H. / Jacobson, R.H. / Wigley, D. / Zhang, X.J. / Huber, R.E. / Tronrud, D.E. / Matthews, B.W.
Citation
Journal: Protein Sci. / Year: 2000
Title: High resolution refinement of beta-galactosidase in a new crystal form reveals multiple metal-binding sites and provides a structural basis for alpha-complementation.
Authors: Juers, D.H. / Jacobson, R.H. / Wigley, D. / Zhang, X.J. / Huber, R.E. / Tronrud, D.E. / Matthews, B.W.
#1: Journal: Protein Sci. / Year: 1999
Title: Structural comparisons of TIM barrel proteins suggest functional and evolutionary relationships between beta-galactosidase and other glycohydrolases
Authors: Juers, D.H. / Jacobson, R.H. / Wigley, D. / Zhang, X.J. / Huber, R.E. / Tronrud, D.E. / Matthews, B.W.
#2: Journal: Nature / Year: 1994
Title: Three-dimensional structure of beta-galactosidase from E. coli
Authors: Juers, D.H. / Huber, R.E. / Matthews, B.W.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization of beta-galactosidase from Escherichia coli
Authors: Jacobson, R.H. / Zhang, X.J. / DuBose, R.F. / Matthews, B.W.
History
DepositionJun 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1F49, 1GHO
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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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)1,867,97248
Polymers1,867,19416
Non-polymers77832
Water125,3846960
1
A: BETA-GALACTOSIDASE
B: BETA-GALACTOSIDASE
C: BETA-GALACTOSIDASE
D: BETA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,99312
Polymers466,7994
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)466,99312
Polymers466,7994
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)466,99312
Polymers466,7994
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)466,99312
Polymers466,7994
Non-polymers1948
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: 116699.641 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BL21 / References: UniProt: P00722, beta-galactosidase
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6960 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: PEG 8000, Cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 20K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. all: 559917 / Num. obs: 559917 / % possible obs: 73 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
WEISdata scaling
WEISdata reduction
TNTrefinement
RefinementHighest resolution: 2.5 Å / Isotropic thermal model: TNT / Stereochemistry target values: TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1516 0.271 %RANDOM WITH NO SPECIAL PRECAUTIONS DUE TO NCS.
Rwork0.199 ---
obs-558194 71 %-
Solvent computationSolvent model: BABINET'S PRINCIPLE / Bsol: 625 Å2 / ksol: 0.98 e/Å3
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms65680 0 16 3480 69176
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0181350401.1
X-RAY DIFFRACTIONt_angle_deg2.71832642
X-RAY DIFFRACTIONt_dihedral_angle_d19.4778720
X-RAY DIFFRACTIONt_trig_c_planes0.01236962
X-RAY DIFFRACTIONt_gen_planes0.015196486
X-RAY DIFFRACTIONt_it5.5313494460
X-RAY DIFFRACTIONt_nbd0.01915283

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