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- PDB-4ogz: Crystal structure of a putative alpha-galactosidase/melibiase (BF... -

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Basic information

Entry
Database: PDB / ID: 4ogz
TitleCrystal structure of a putative alpha-galactosidase/melibiase (BF4189) from Bacteroides fragilis NCTC 9343 at 2.00 A resolution
ComponentsPutative alpha-galactosidase/melibiase
KeywordsHYDROLASE / Putative catalytic domain (TIM beta/alpha-barrel fold ) accompanied by two Ig-like domains. Two Pfam hits on N-terminus: NEW1 domain (PF10632) and melibiase domain (PF02065). / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


alpha-galactosidase / alpha-galactosidase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Alpha galactosidase, C-terminal beta sandwich domain / Alpha galactosidase C-terminal beta sandwich domain / Putative Ig 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 ...Alpha galactosidase, C-terminal beta sandwich domain / Alpha galactosidase C-terminal beta sandwich domain / Putative Ig 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 fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Alpha-galactosidase
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative alpha-galactosidase/melibiase (BF4189) from Bacteroides fragilis NCTC 9343 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.4Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative alpha-galactosidase/melibiase
B: Putative alpha-galactosidase/melibiase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,48013
Polymers106,2352
Non-polymers1,24411
Water8,323462
1
A: Putative alpha-galactosidase/melibiase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7366
Polymers53,1181
Non-polymers6195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative alpha-galactosidase/melibiase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7437
Polymers53,1181
Non-polymers6266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Putative alpha-galactosidase/melibiase
hetero molecules

A: Putative alpha-galactosidase/melibiase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,48013
Polymers106,2352
Non-polymers1,24411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_857-x+3,y+1/2,-z+21
Buried area4390 Å2
ΔGint16 kcal/mol
Surface area33690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.955, 170.874, 52.619
Angle α, β, γ (deg.)90.000, 106.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative alpha-galactosidase/melibiase


Mass: 53117.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF9343_4081, YP_213754.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5L7T7, alpha-galactosidase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 25-496) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 25-496) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 50.0% polyethylene glycol 200, 0.2M sodium chloride, 0.1M phosphate-citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.918401,0.979183
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2013 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9184011
20.9791831
ReflectionResolution: 2→56.958 Å / Num. all: 57998 / Num. obs: 57998 / % possible obs: 100 % / Redundancy: 3.7 % / Rsym value: 0.183 / Net I/σ(I): 4.1
Reflection shell

Rmerge(I) obs: 0.012 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.053.70.41599642901.176100
2.05-2.113.70.61558241880.886100
2.11-2.173.70.81495040110.711100
2.17-2.243.711474639630.592100
2.24-2.313.71.11428538450.484100
2.31-2.393.71.51374536920.398100
2.39-2.483.71.71325835590.352100
2.48-2.583.721275734320.301100
2.58-2.73.72.11228732990.262100
2.7-2.833.72.81165731440.209100
2.83-2.983.73.51102529850.168100
2.98-3.163.73.81039528190.145100
3.16-3.383.74.4977426730.12999.9
3.38-3.653.64.6909825020.114100
3.65-43.54.6796522620.096100
4-4.473.55.4733720780.085100
4.47-5.163.75.9676418380.073100
5.16-6.323.75.8571015410.076100
6.32-8.943.85.6461112060.078100
8.94-56.9583.74.324646710.08799.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.20data scaling
REFMAC5.7.0029refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2→56.958 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 9.363 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.154
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2 .A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2 .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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.POLYETHYLENE GLYCOL FRAGMENTS (PEG, PGE) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE. 6.PHOSPHATE (PO4),MOST LIKELY FROM THE EXPRESSION BUFFERS HAS BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2006 2942 5.1 %RANDOM
Rwork0.1692 ---
obs0.1708 57884 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 125.59 Å2 / Biso mean: 24.5617 Å2 / Biso min: 8.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å2-2.31 Å2
2---1.12 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 2→56.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7200 0 81 462 7743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197505
X-RAY DIFFRACTIONr_bond_other_d0.0040.027153
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.97510161
X-RAY DIFFRACTIONr_angle_other_deg0.943316478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4585942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11824.207328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84151193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6071545
X-RAY DIFFRACTIONr_chiral_restr0.0540.21088
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218466
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021675
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 237 -
Rwork0.291 4011 -
all-4248 -
obs--99.11 %
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)
10.4757-0.23990.27760.6642-0.16660.55710.0102-0.0548-0.00320.04630.00380.01840.0213-0.0411-0.0140.0212-0.00930.03060.0741-0.00720.058266.560685.339746.5167
20.37850.11340.17190.51610.06010.4731-0.00130.0033-0.02470.02410.0037-0.03490.00990.0283-0.00240.02360.01070.03370.07060.00140.061451.2083127.347159.8448
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 496
2X-RAY DIFFRACTION2B25 - 496

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