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- PDB-3cc1: CRYSTAL STRUCTURE OF A PUTATIVE ALPHA-N-ACETYLGALACTOSAMINIDASE (... -

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Basic information

Entry
Database: PDB / ID: 3cc1
TitleCRYSTAL STRUCTURE OF A PUTATIVE ALPHA-N-ACETYLGALACTOSAMINIDASE (BH1870) FROM BACILLUS HALODURANS C-125 AT 2.00 A RESOLUTION
ComponentsPutative alpha-N-acetylgalactosaminidase
KeywordsHYDROLASE / PUTATIVE ALPHA-N-ACETYLGALACTOSAMINIDASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


raffinose alpha-galactosidase activity / alpha-galactosidase / carbohydrate metabolic process
Similarity search - Function
Alpha galactosidase, C-terminal beta sandwich domain / Alpha galactosidase C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel ...Alpha galactosidase, C-terminal beta sandwich domain / Alpha galactosidase C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Alpha-galactosidase
Similarity search - Component
Biological speciesBacillus halodurans C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative alpha-N-acetylgalactosaminidase (NP_242736.1) from Bacillus halodurans at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative alpha-N-acetylgalactosaminidase
B: Putative alpha-N-acetylgalactosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,77627
Polymers100,7622
Non-polymers3,01425
Water12,448691
1
A: Putative alpha-N-acetylgalactosaminidase
B: Putative alpha-N-acetylgalactosaminidase
hetero molecules

A: Putative alpha-N-acetylgalactosaminidase
B: Putative alpha-N-acetylgalactosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,55354
Polymers201,5254
Non-polymers6,02850
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area12840 Å2
ΔGint-71.5 kcal/mol
Surface area59390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.943, 146.943, 213.526
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-433-

SO4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative alpha-N-acetylgalactosaminidase / / BH1870 protein


Mass: 50381.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans C-125 (bacteria) / Species: Bacillus halodurans / Strain: C-125 / DSM 18197 / FERM 7344 / JCM 9153 / Gene: NP_242736.1, BH1870 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q9KBQ5, alpha-N-acetylgalactosaminidase

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Non-polymers , 8 types, 716 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. DNA SEQUENCING REVEALED THAT RESIDUE 272 WAS GLY AND RESIDUE 311 WAS HIS IN THE CLONED CONSTRUCT.

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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: 3.3 Å3/Da / Density % sol: 62.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: NANODROP, 0.2M (NH4)2SO4, 10.0% Glycerol, 20.0% PEG 300, 0.1M Phosphate citrate pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91840, 0.97953, 0.97939
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.979531
30.979391
ReflectionResolution: 2→34.816 Å / Num. obs: 91976 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 25.207 Å2 / Rmerge(I) obs: 0.153 / Rsym value: 0.153 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.0511.11.0080.87479067201.008100
2.05-2.1111.10.8190.97249065230.819100
2.11-2.1711.10.6641.27041863250.664100
2.17-2.2411.10.5581.46899862030.558100
2.24-2.3111.10.4581.66639059840.458100
2.31-2.3911.10.37326458158020.373100
2.39-2.4811.10.3372.26234656030.337100
2.48-2.5811.10.2882.66004354170.288100
2.58-2.711.10.2372.95752751890.237100
2.7-2.83110.1963.85524850000.196100
2.83-2.98110.1544.75225047290.154100
2.98-3.16110.1255.74984145120.125100
3.16-3.38110.1066.34670942390.106100
3.38-3.6510.90.16.24331939740.1100
3.65-410.80.0887.13953736560.088100
4-4.4710.90.0737.83644633590.073100
4.47-5.1610.80.0718.23198929600.071100
5.16-6.3210.60.0738.22717225570.073100
6.32-8.9410.30.0619.22085920280.061100
8.94-34.8169.40.05991119311960.05998.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→34.816 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.346 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.115
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SULFATE, GLYCEROL, PARTIAL PEG 300 AND IMIDAZOLE FROM CRYSTALLIZATION CONDITION ARE MODELED IN THIS STRUCTURE. 5. UNKNOWN Y-SHAPE ELECTRON DENSITY IS OBSERVED NEAR RESIDUE 18 AND RESIDUE 112 IN SUBUNIT B.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 4602 5 %RANDOM
Rwork0.162 ---
obs0.164 91891 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.091 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20.47 Å20 Å2
2--0.93 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 2→34.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6735 0 192 691 7618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227254
X-RAY DIFFRACTIONr_bond_other_d0.0010.024955
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9549820
X-RAY DIFFRACTIONr_angle_other_deg1.034312012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33323.958331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.203151131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9371540
X-RAY DIFFRACTIONr_chiral_restr0.0940.21009
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218019
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021495
X-RAY DIFFRACTIONr_mcbond_it0.8021.54335
X-RAY DIFFRACTIONr_mcbond_other0.2161.51752
X-RAY DIFFRACTIONr_mcangle_it1.45326982
X-RAY DIFFRACTIONr_scbond_it2.42132919
X-RAY DIFFRACTIONr_scangle_it3.7754.52838
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 353 -
Rwork0.226 6365 -
all-6718 -
obs--100 %
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)
10.8978-0.31310.64550.30130.21391.5428-0.03020.09940.0545-0.10160.0767-0.0384-0.09890.2909-0.0466-0.0533-0.0499-0.00030.0406-0.0195-0.063787.784317.782821.8871
20.6344-0.0834-0.19270.60830.18121.3274-0.05290.0054-0.082-0.03910.0482-0.00480.11480.19190.0047-0.04870.0165-0.0124-0.0161-0.0199-0.072778.62532.638217.8332
30.51840.07930.58790.4138-0.121.0581-0.04150.04260.0646-0.02610.0042-0.0263-0.09540.13450.0372-0.0743-0.0377-0.00460.0343-0.0307-0.044689.197421.682541.9998
40.70420.02320.31350.7550.11011.94890.0386-0.0839-0.1445-0.1270.01150.06160.1234-0.0781-0.05-0.0564-0.0155-0.0524-0.08790.0474-0.004142.2981-0.4927.5709
50.80380.0111-0.00870.5766-0.16440.76850.04160.0161-0.0567-0.05990.02010.02710.05980.0029-0.0617-0.04110.0066-0.0301-0.05920.0154-0.029549.532611.816620.2739
60.43740.13280.380.48290.2861.12960.0871-0.1739-0.13430.06060.01590.06040.2809-0.1365-0.103-0.0416-0.0462-0.0504-0.02980.09850.010147.3825-5.223748.1878
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 57
2X-RAY DIFFRACTION2A58 - 240
3X-RAY DIFFRACTION3A241 - 432
4X-RAY DIFFRACTION4B0 - 70
5X-RAY DIFFRACTION5B71 - 238
6X-RAY DIFFRACTION6B239 - 431

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