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- PDB-5dmy: Beta-galactosidase - construct 33-930 -

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Basic information

Entry
Database: PDB / ID: 5dmy
TitleBeta-galactosidase - construct 33-930
ComponentsBeta-galactosidase
KeywordsHYDROLASE / galactosidase / truncation mutant
Function / homology
Function and homology information


beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Bacterial Ig-like domain / Bacterial Ig-like domain (group 4) / Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / Invasin/intimin cell-adhesion fragments / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain ...Bacterial Ig-like domain / Bacterial Ig-like domain (group 4) / Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / Invasin/intimin cell-adhesion fragments / 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 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / 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
NICKEL (II) ION / Beta-galactosidase
Similarity search - Component
Biological speciesBifidobacterium bifidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWatson, K.A. / Lazidou, A.
CitationJournal: To Be Published
Title: Rational protein engineering toward the development of a beta-galactosidase with improved functional properties
Authors: Lazidou, A. / Charalampopoulos, D. / Watson, K.A.
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,57114
Polymers294,1973
Non-polymers37311
Water44,4792469
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-89 kcal/mol
Surface area90220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.040, 52.650, 153.329
Angle α, β, γ (deg.)90.00, 91.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Beta-galactosidase


Mass: 98065.734 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: HHHHHHVEDATRSDSTTQMSSTPEVVYSSAVDSK QNRTSDFDANWKFMLSDSVQAQDPAFDDSAWQQVDLPHDYSITQKYSQSNEAESAYLPGG TGWYRKSFTIDRDLAGKRIAINFDGVYMNATVWFNGVKLGTHPYGYSPFSFDLTGNAKFG ...Details: HHHHHHVEDATRSDSTTQMSSTPEVVYSSAVDSK QNRTSDFDANWKFMLSDSVQAQDPAFDDSAWQQVDLPHDYSITQKYSQSNEAESAYLPGG TGWYRKSFTIDRDLAGKRIAINFDGVYMNATVWFNGVKLGTHPYGYSPFSFDLTGNAKFG GENTIVVKVENRLPSSRWYSGSGIYRDVTLTVTDGVHVGNNGVAIKTPSLATQNGGNVTM NLTTKVANDTEAAANITLKQTVFPKGGKTDAAIGTVTTASKSIAAGASADVTSTITAASP KLWSIKNPNLYTVRTEVLNGDTVLDTYDTEYGFRWTGFDATSGFSLNGEKVKLKGVSMHH DQGSLGAVANRRAIERQVEILQKMGVNSIRTTHNPAAKALIDVCNEKGVLVVEEVFDMWN RSKNGNTEDYGKWFGQTIAGDNAVLGGDKDETWAKFDLTSTINRDRNAPSVIMWSLGNEM MEGISGSVSDFPATSAKLVAWTKAADSTRPMTYGDNKIKANWNESNTMGDNLTANGGVVG TNYSDGANYDKIRTTHPSWAIYGSETASAINSRGIYNRTTGGAQSSDKQLTSYDNSAVGW GAVASSAWYDVVQRDFVAGTYVWTGFDYLGEPTPWNGTGSGAVGSWPSPKNSYFGIVDTA GFPKDTYYFYQSQWNDDVHTLHILPAWNENVVAKGSGNKVPVVVYTDAAKVKLYFTPKGS TEKRLIGEKSFTKKTTAAGYTYQVYEGTDKDSTAHKNMYLTWNVPWAEGTISAEAYDENN RLIPEGSTEGNASVTTTGKAAKLKADADRKTITADGKDLSYIEVDVTDANGHIVPDAANR VTFDVKGAGKLVGVDNGSSPDHDSYQADNRKAFSGKVLAIVQSTKEAGEITVTAKADGLQ SSTVKIATTAVPGTSTEKTVRSFYYSRNYY
Source: (gene. exp.) Bifidobacterium bifidum (bacteria) / Gene: bbgIII / Production host: Escherichia coli (E. coli) / References: UniProt: D4QAP3, beta-galactosidase

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Non-polymers , 5 types, 2480 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2469 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG 6000, 0.1M MES, 0.2M NaCl, pH6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97858 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97858 Å / Relative weight: 1
ReflectionResolution: 1.95→54.93 Å / Num. obs: 170170 / % possible obs: 95.2 % / Redundancy: 2.8 % / Net I/σ(I): 5.1
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.4 / % possible all: 87.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 1.95→54.928 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 8533 5.01 %Random selection
Rwork0.1982 ---
obs0.2016 170170 94.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→54.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19365 0 17 2469 21851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819866
X-RAY DIFFRACTIONf_angle_d1.09227096
X-RAY DIFFRACTIONf_dihedral_angle_d12.3386877
X-RAY DIFFRACTIONf_chiral_restr0.0433023
X-RAY DIFFRACTIONf_plane_restr0.0043521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.35042480.26174804X-RAY DIFFRACTION87
1.9722-1.99540.32972520.25944892X-RAY DIFFRACTION86
1.9954-2.01970.31572570.24864898X-RAY DIFFRACTION86
2.0197-2.04530.32262510.24714796X-RAY DIFFRACTION87
2.0453-2.07220.33062460.2434932X-RAY DIFFRACTION87
2.0722-2.10060.31862800.23644959X-RAY DIFFRACTION87
2.1006-2.13060.30122680.23654933X-RAY DIFFRACTION88
2.1306-2.16240.29212770.24144946X-RAY DIFFRACTION88
2.1624-2.19620.30242730.22975105X-RAY DIFFRACTION90
2.1962-2.23220.28512530.21745044X-RAY DIFFRACTION91
2.2322-2.27070.272680.21085242X-RAY DIFFRACTION92
2.2707-2.3120.31172830.20735304X-RAY DIFFRACTION94
2.312-2.35640.2752880.20585389X-RAY DIFFRACTION96
2.3564-2.40450.28112730.20465575X-RAY DIFFRACTION98
2.4045-2.45680.27453100.2045579X-RAY DIFFRACTION99
2.4568-2.5140.26182790.20135658X-RAY DIFFRACTION99
2.514-2.57680.28923150.21735554X-RAY DIFFRACTION99
2.5768-2.64650.29932900.2135697X-RAY DIFFRACTION99
2.6465-2.72440.30012950.20045514X-RAY DIFFRACTION99
2.7244-2.81230.2683370.1975634X-RAY DIFFRACTION100
2.8123-2.91280.26862900.20825666X-RAY DIFFRACTION100
2.9128-3.02940.26622950.21165628X-RAY DIFFRACTION100
3.0294-3.16730.2822810.20235690X-RAY DIFFRACTION99
3.1673-3.33430.25753240.19085664X-RAY DIFFRACTION100
3.3343-3.54310.25612740.18895699X-RAY DIFFRACTION100
3.5431-3.81660.23542860.17615697X-RAY DIFFRACTION100
3.8166-4.20060.2043010.15185718X-RAY DIFFRACTION100
4.2006-4.80810.18922900.14145788X-RAY DIFFRACTION100
4.8081-6.05650.20413220.14965727X-RAY DIFFRACTION99
6.0565-54.95010.19113270.16445905X-RAY DIFFRACTION99

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