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- PDB-3u7v: The structure of a putative Beta-galactosidase from Caulobacter c... -

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Basic information

Entry
Database: PDB / ID: 3u7v
TitleThe structure of a putative Beta-galactosidase from Caulobacter crescentus CB15.
ComponentsBeta-galactosidase
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / TIM barrel / Glyco_hydro_42 / Carbohydrate transport and metabolism
Function / homology
Function and homology information


beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
putative beta-Galactosidase from caulobacter crescentus / Domain of unknown function DUF5597 / Domain of unknown function (DUF5597) / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Glycoside hydrolase, family 35 / Chondroitinase Ac; Chain A, domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...putative beta-Galactosidase from caulobacter crescentus / Domain of unknown function DUF5597 / Domain of unknown function (DUF5597) / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Glycoside hydrolase, family 35 / Chondroitinase Ac; Chain A, domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Beta-galactosidase / Beta-galactosidase
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsCuff, M.E. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of a putative Beta-galactosidase from Caulobacter crescentus CB15.
Authors: Cuff, M.E. / Tesar, C. / Clancy, S. / Joachimiak, A.
History
DepositionOct 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Nov 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2343
Polymers61,1141
Non-polymers1202
Water7,692427
1
A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,93712
Polymers244,4574
Non-polymers4808
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area9510 Å2
ΔGint-27 kcal/mol
Surface area72810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.306, 148.306, 53.792
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Detailslikely the tetramer formed in the crystal x,y,z , y,-x,z , -y,x,z , -x,-y,z

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Components

#1: Protein Beta-galactosidase


Mass: 61114.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: NA1000 / Gene: CCNA_00830, LacA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic
References: UniProt: B8H1H2, UniProt: A0A0H3C5N2*PLUS, beta-galactosidase
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.17 Amonium sulfate, 0.085 sodium citrate: HCl pH 5.6, 25.5% PEG 4K, 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionRedundancy: 7.8 % / Av σ(I) over netI: 21.84 / Number: 422096 / Rmerge(I) obs: 0.116 / Χ2: 1.21 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 54354 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.885099.510.092.5037.2
3.884.8810010.0842.0747.3
3.393.8810010.0922.2227.5
3.083.3999.910.1022.1787.7
2.863.0810010.1091.8417.8
2.692.8610010.1141.67.8
2.552.6910010.1181.4277.9
2.442.5510010.1251.2557.9
2.352.4410010.1371.1657.9
2.272.3510010.1441.0787.9
2.22.2710010.1520.9447.9
2.132.210010.1620.9097.9
2.082.1310010.1760.8427.9
2.032.0810010.1890.7577.9
1.982.0310010.2120.6887.9
1.941.9810010.240.6247.9
1.91.9410010.2840.5767.9
1.861.910010.3050.5557.8
1.831.8610010.3570.5337.9
1.81.8310010.3980.517.8
ReflectionResolution: 1.8→50 Å / Num. all: 54354 / Num. obs: 54354 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.116 / Χ2: 1.205 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.837.80.39827250.511100
1.83-1.867.90.35726900.5331100
1.86-1.97.80.30526860.5551100
1.9-1.947.90.28427130.5761100
1.94-1.987.90.2426940.6241100
1.98-2.037.90.21226620.6881100
2.03-2.087.90.18927430.7571100
2.08-2.137.90.17626970.8421100
2.13-2.27.90.16226850.9091100
2.2-2.277.90.15227000.9441100
2.27-2.357.90.14427361.0781100
2.35-2.447.90.13727131.1651100
2.44-2.557.90.12527021.2551100
2.55-2.697.90.11827261.4271100
2.69-2.867.80.11427101.61100
2.86-3.087.80.10927171.8411100
3.08-3.397.70.10227362.178199.9
3.39-3.887.50.09227422.2221100
3.88-4.887.30.08427642.0741100
4.88-507.20.0928132.503199.5

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2 Å / D res low: 50 Å / FOM : 0.259 / FOM acentric: 0.274 / FOM centric: 0 / Reflection: 39779 / Reflection acentric: 37631 / Reflection centric: 2148
Phasing MAD setR cullis acentric: 1.3 / R cullis centric: 1 / Highest resolution: 2 Å / Lowest resolution: 50 Å / Loc acentric: 0.2 / Loc centric: 0.2 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 37631 / Reflection centric: 2148
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
12.5-501.240.40.312746
7.14-12.51.220.40.3631112
5-7.141.30.30.31547174
3.85-50.940.30.32839242
3.13-3.851.050.30.34580298
2.63-3.131.450.20.26654363
2.27-2.631.520.20.19166427
2-2.271.50.10.112087486
Phasing MAD set site

Atom type symbol: Se / Occupancy iso: 0

IDB isoFract xFract yFract zOccupancy
115.53460.0030.650.092.163
214.85440.8810.6550.2862.302
319.10110.2340.1920.3212.117
415.51110.6670.0120.0041.989
58.5750.290.550.4951.779
615.80810.6880.8810.0371.978
727.05160.0440.7040.1312.027
815.07510.2710.050.1161.786
914.76170.8090.8620.1311.795
108.61640.7710.1570.2931.671
1117.1470.7080.1530.2681.787
1212.34810.5420.1620.4451.783
1315.11810.7390.1810.3841.814
1430.78690.9810.2450.5051.759
1530.75770.1760.0040.2081.282
1644.7150.2490.1940.3690.637
1753.6360.8410.6640.3010.571
1829.8820.4150.6390.0050.432
1925.7210.7880.8730.1290.362
2044.0950.2230.0750.0160.496
2124.0540.2370.5640.0770.264
2250.6610.260.030.1340.46
2324.9870.3630.0490.0880.272
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.5-500.250.34017312746
7.14-12.50.2770.3260743631112
5-7.140.3370.375017211547174
3.85-50.2850.31030812839242
3.13-3.850.270.287048784580298
2.63-3.130.3120.329070176654363
2.27-2.630.2730.286095939166427
2-2.270.1960.20401257312087486
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 54349
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.68-10066.90.756524
6.48-8.6864.60.906708
5.4-6.4862.10.918865
4.72-5.4630.9371015
4.25-4.7259.70.9511141
3.9-4.25630.9411239
3.62-3.9610.9361352
3.39-3.6264.30.9421429
3.21-3.3965.80.9281545
3.05-3.2161.90.9281607
2.91-3.0562.10.9191682
2.79-2.9162.80.9231751
2.68-2.7962.40.9271849
2.58-2.6865.10.9291876
2.5-2.5864.90.9171994
2.42-2.564.50.9252030
2.35-2.4265.50.922077
2.28-2.3564.60.9152171
2.22-2.2867.50.922208
2.17-2.22690.9182251
2.12-2.17710.9142365
2.07-2.1271.30.9132325
2.02-2.0772.20.9172468
1.98-2.0279.90.9032477
1.94-1.9889.30.9022536
1.9-1.9490.80.872580
1.87-1.988.40.8382620
1.84-1.8790.50.7642658
1.8-1.8488.90.5673006

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→36.4 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.2147 / WRfactor Rwork: 0.1823 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9067 / SU B: 4.319 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1226 / SU Rfree: 0.1158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.116
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 2764 5.1 %RANDOM
Rwork0.1838 ---
all0.1854 54352 --
obs0.1854 54352 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.46 Å2 / Biso mean: 18.6393 Å2 / Biso min: 10.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2---0.78 Å20 Å2
3---1.56 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4015 0 8 427 4450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.024153
X-RAY DIFFRACTIONr_bond_other_d0.0020.022811
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9455654
X-RAY DIFFRACTIONr_angle_other_deg0.89936817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4125520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2723.85187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55515638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6711525
X-RAY DIFFRACTIONr_chiral_restr0.0970.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214718
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02891
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 191 -
Rwork0.171 3628 -
all-3819 -
obs--99.25 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42230.2119-0.01730.40960.0160.12680.0037-0.01140.04310.0184-0.0104-0.0032-0.00920.00740.00670.0270.0039-0.00890.0139-0.00240.0094-1.435141.951113.6766
20.78320.38880.02170.517-0.02010.142-0.01990.00770.0550.0260.0080.10570.0382-0.0380.0120.0391-0.00620.00050.0302-0.00810.0326-29.06824.089313.0444
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 460
2X-RAY DIFFRACTION2A461 - 549

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