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- PDB-3k11: Crystal structure of Putative glycosyl hydrolase (NP_813087.1) fr... -

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Basic information

Entry
Database: PDB / ID: 3k11
TitleCrystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution
ComponentsPutative glycosyl hydrolase
KeywordsHYDROLASE / Putative glycosyl hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / unknown function
Function / homology
Function and homology information


carbohydrate metabolic process
Similarity search - Function
: / Glycosyl hydrolase, family 88 / Glycosyl Hydrolase Family 88 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Glycoside hydrolase family 88 protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of Putative glycosyl hydrolase (NP_813087.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 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 17, 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
Revision 1.5Nov 20, 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

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Assembly

Deposited unit
A: Putative glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,17921
Polymers50,8051
Non-polymers1,37520
Water8,431468
1
A: Putative glycosyl hydrolase
hetero molecules

A: Putative glycosyl hydrolase
hetero molecules

A: Putative glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,53863
Polymers152,4143
Non-polymers4,12460
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area21320 Å2
ΔGint136 kcal/mol
Surface area44890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.135, 121.135, 182.812
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

21A-689-

HOH

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Components

#1: Protein Putative glycosyl hydrolase


Mass: 50804.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_4176 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A045
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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. THE CLONED CONSTRUCT CONTAINS RESIDUES 22-465 OF THE FULL LENGTH PROTEIN.

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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: 3.81 Å3/Da / Density % sol: 67.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 5.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97936,0.97919
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 15, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979361
30.979191
ReflectionResolution: 1.8→29.988 Å / Num. obs: 73725 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 22.138 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.857.30.76413918153330.764100
1.85-1.97.40.6211.23852452410.621100
1.9-1.957.30.4961.63739350930.496100
1.95-2.017.40.38423641049430.384100
2.01-2.087.40.3232.43538548100.323100
2.08-2.157.40.25333418646490.253100
2.15-2.237.40.2163.53301044860.216100
2.23-2.327.40.1794.13189143370.179100
2.32-2.437.30.1524.83063241700.152100
2.43-2.557.40.1285.52922839750.128100
2.55-2.687.30.1136.32789138020.113100
2.68-2.857.30.0996.72638036120.099100
2.85-3.047.30.0897.12482834120.089100
3.04-3.297.20.0837.52306331830.083100
3.29-3.67.20.0669.22134029460.066100
3.6-4.027.20.05810.11934926820.058100
4.02-4.657.20.053111714723980.053100
4.65-5.6970.05610.41436620500.056100
5.69-8.056.80.05610.21108516390.056100
8.05-306.10.04711.959169640.04798.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.988 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.425 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.077
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.2-(N-MORPHOLINO)ETHANESULFONIC ACID (MES)AND ETHYLENE GLYCOL (EDO) MOLECULES MODELED IN THE STRUCTURE WERE PRESENT IN CRYSTALLIZATION BUFFER/CRYOPROTECTANT.
RfactorNum. reflection% reflectionSelection details
Rfree0.171 3714 5 %RANDOM
Rwork0.15 ---
obs0.151 73676 99.96 %-
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: 85.14 Å2 / Biso mean: 29.571 Å2 / Biso min: 13.23 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20.81 Å20 Å2
2--1.61 Å20 Å2
3----2.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3489 0 88 468 4045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223821
X-RAY DIFFRACTIONr_bond_other_d0.0030.022614
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9495181
X-RAY DIFFRACTIONr_angle_other_deg1.0836317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0385472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44323.704189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36815596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6151527
X-RAY DIFFRACTIONr_chiral_restr0.1010.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024349
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02825
X-RAY DIFFRACTIONr_nbd_refined0.2250.3845
X-RAY DIFFRACTIONr_nbd_other0.1850.32831
X-RAY DIFFRACTIONr_nbtor_refined0.1910.51911
X-RAY DIFFRACTIONr_nbtor_other0.0890.51829
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.5648
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.315
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.397
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.560
X-RAY DIFFRACTIONr_mcbond_it1.98832448
X-RAY DIFFRACTIONr_mcbond_other0.5493920
X-RAY DIFFRACTIONr_mcangle_it2.53553692
X-RAY DIFFRACTIONr_scbond_it4.81981726
X-RAY DIFFRACTIONr_scangle_it6.089111489
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 260 -
Rwork0.219 5066 -
all-5326 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 17.1713 Å / Origin y: 48.4717 Å / Origin z: 21.7161 Å
111213212223313233
T-0.0208 Å20.0426 Å20.0165 Å2--0.0442 Å2-0.0065 Å2---0.0177 Å2
L0.3503 °2-0.1002 °2-0.0358 °2-0.1303 °20.0322 °2--0.4833 °2
S-0.0172 Å °0.0223 Å °-0.0716 Å °-0.0127 Å °-0.0035 Å °-0.0159 Å °0.1506 Å °0.0888 Å °0.0207 Å °

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