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- PDB-3gyc: Crystal structure of putative glycoside hydrolase (YP_001304622.1... -

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Basic information

Entry
Database: PDB / ID: 3gyc
TitleCrystal structure of putative glycoside hydrolase (YP_001304622.1) from Parabacteroides distasonis ATCC 8503 at 1.85 A resolution
ComponentsPutative glycoside hydrolase
KeywordsHYDROLASE / YP_001304622.1 / putative glycoside hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyPutative cellulase / Sugar-binding cellulase-like / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesParabacteroides distasonis ATCC 8503 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative glycoside hydrolase (YP_001304622.1) from Parabacteroides distasonis ATCC 8503 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_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 glycoside hydrolase
B: Putative glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0018
Polymers93,6292
Non-polymers3726
Water7,476415
1
A: Putative glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0635
Polymers46,8141
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9393
Polymers46,8141
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.209, 84.915, 77.991
Angle α, β, γ (deg.)90.000, 94.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative glycoside hydrolase /


Mass: 46814.492 Da / Num. of mol.: 2 / Fragment: UNP residues 28-419
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis ATCC 8503 (bacteria)
Strain: DSM 20701 / NCTC 11152 / Gene: BDI_3295, YP_001304622.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LH36
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT IS COMPRISED OF RESIDUES 28-419 OF THE FULL-LENGTH PROTEIN. IT WAS EXPRESSED WITH A ...THIS CONSTRUCT IS COMPRISED OF RESIDUES 28-419 OF THE FULL-LENGTH PROTEIN. IT 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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: NANODROP, 20.0% PEG 3000, 0.1M Citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.91162, 0.97954
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 29, 2009
Details: Flat mirror, vertical and horizontal focusing mirrors
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979541
ReflectionResolution: 1.85→29.604 Å / Num. obs: 66845 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.93.80.671.91864249460.67100
1.9-1.953.80.5812.21801147760.581100
1.95-2.013.80.4562.81766646810.456100
2.01-2.073.80.363.41716045380.36100
2.07-2.143.80.3034.11661543820.303100
2.14-2.213.80.2514.91618542670.251100
2.21-2.293.80.2075.81549740960.207100
2.29-2.393.80.1736.81501139520.173100
2.39-2.493.80.1517.71451338190.151100
2.49-2.623.80.1249.41373936160.124100
2.62-2.763.80.10711.11309634410.107100
2.76-2.933.80.09612.51236032460.096100
2.93-3.133.80.076151176330950.076100
3.13-3.383.80.06517.31086628700.065100
3.38-3.73.80.05619.71001026470.056100
3.7-4.143.80.04921.8900223890.049100
4.14-4.783.80.05223.5794521130.052100
4.78-5.853.70.05324.6665517840.053100
5.85-8.273.70.04625.5520214130.046100
8.27-29.6043.60.04326.627547740.04397.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→29.604 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 7.77 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.126
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ELECTRON DENSITY INDICATES THAT THE PEPTIDE BOND BETWEEN CYS 332 AND TRP 333 IN BOTH SUBUNITS IN THE ASYMMETRIC UNIT IS IN THE CIS-CONFIGURATION. THIS IS IN THE VICINITY OF THE PUTATIVE ACTIVE SITE. 5. 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTION CONDITION HAS BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 3384 5.1 %RANDOM
Rwork0.169 ---
obs0.171 66817 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 max: 57.13 Å2 / Biso mean: 16.106 Å2 / Biso min: 5.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å2-1.03 Å2
2--1.67 Å20 Å2
3----2.11 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6269 0 24 415 6708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226585
X-RAY DIFFRACTIONr_bond_other_d0.0020.024511
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9368981
X-RAY DIFFRACTIONr_angle_other_deg0.966310902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0855790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.48323.681326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.338151089
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.851546
X-RAY DIFFRACTIONr_chiral_restr0.1060.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217328
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021428
X-RAY DIFFRACTIONr_mcbond_it1.08523849
X-RAY DIFFRACTIONr_mcbond_other0.30321544
X-RAY DIFFRACTIONr_mcangle_it1.70436229
X-RAY DIFFRACTIONr_scbond_it1.35422736
X-RAY DIFFRACTIONr_scangle_it1.99732737
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 246 -
Rwork0.272 4670 -
all-4916 -
obs--99.66 %
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)
10.94710.51620.97651.50031.36012.83110.1291-0.0056-0.06380.4031-0.0132-0.11910.48410.0659-0.11590.13770.0087-0.00230.04380.00970.058514.725659.0948-6.2002
20.8340.59270.5731.58261.16722.6645-0.1017-0.00160.14-0.3695-0.22030.3806-0.4781-0.29530.32190.1280.0912-0.07360.1107-0.06110.1453-7.416156.9164-43.743
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 419
2X-RAY DIFFRACTION2B39 - 419

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