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- PDB-4qhb: Crystal structure of a putative hydrolase (BVU_2763) from Bactero... -

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Basic information

Entry
Database: PDB / ID: 4qhb
TitleCrystal structure of a putative hydrolase (BVU_2763) from Bacteroides vulgatus ATCC 8482 at 2.44 A resolution
ComponentsUncharacterized protein
KeywordsHYDROLASE / two domain protein / N-glycanase_Nterm (PF09112) and N-glycanase_Cterm (PF09113) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen
Similarity search - Function
Peptide-N-glycosidase F, N-terminal domain / Peptide-N-glycosidase F, N-terminal domain superfamily / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, N-terminal / Peptide-N-glycosidase F, C-terminal / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, C terminal / Jelly Rolls - #230 / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal ...Peptide-N-glycosidase F, N-terminal domain / Peptide-N-glycosidase F, N-terminal domain superfamily / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, N-terminal / Peptide-N-glycosidase F, C-terminal / Peptide-N-glycosidase F, N terminal / Peptide-N-glycosidase F, C terminal / Jelly Rolls - #230 / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / N-glycanase_N domain-containing protein
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.44 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BVU_2763) from Bacteroides vulgatus ATCC 8482 at 2.44 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,39217
Polymers179,9304
Non-polymers1,46113
Water11,494638
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12070 Å2
ΔGint-109 kcal/mol
Surface area61010 Å2
MethodPISA
2
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,97811
Polymers89,9652
Non-polymers1,0139
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-55 kcal/mol
Surface area31640 Å2
MethodPISA
3
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4136
Polymers89,9652
Non-polymers4484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-46 kcal/mol
Surface area31400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.102, 107.296, 108.137
Angle α, β, γ (deg.)90.000, 101.820, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Uncharacterized protein


Mass: 44982.535 Da / Num. of mol.: 4 / Fragment: UNP residues 23-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_2763 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6L3Z9

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Non-polymers , 5 types, 651 molecules

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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING GLY 0 FOLLOWED BY RESIDUES 23-416 OF 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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.050M lithium sulfate, 10.00% Glycerol, 30.00% polyethylene glycol 600, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.96109,0.97934,0.97911
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 26, 2014
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961091
20.979341
30.979111
ReflectionResolution: 2.44→47.852 Å / Num. obs: 69089 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.515 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.79
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.44-2.530.6052.1224427091199.7
2.53-2.630.4832.62157667661100
2.63-2.750.3893.32202368991100
2.75-2.890.2984.2212066652199.8
2.89-3.070.2345.32197768941100
3.07-3.310.1557.7222647023199.8
3.31-3.640.09311.5216816820199.9
3.64-4.160.0714.4221006916199.8
4.16-5.230.05317.9220986936199.7
5.23-47.8520.05818.5224047092199.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMAC5.7.0029refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.44→47.852 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.552 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.415 / ESU R Free: 0.238
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. 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 ...Details: 1. 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. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. ATOM RECORD CONTAINS 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. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD (MOTION DETERMINATION) SERVER. 6. POLYETHYLENE GLYCOL FRAGMENTS (PEG, PGE,PG4), AND SULFATE (SO4) FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3499 5.1 %RANDOM
Rwork0.17 ---
obs0.1723 69063 99.79 %-
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: 119.57 Å2 / Biso mean: 36.9303 Å2 / Biso min: 6.26 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å2-1.1 Å2
2--2.48 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.44→47.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12260 0 88 638 12986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01912689
X-RAY DIFFRACTIONr_bond_other_d0.0060.0211942
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.97417254
X-RAY DIFFRACTIONr_angle_other_deg1.1323.00127550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.09651557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72223.838555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.582151970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2341579
X-RAY DIFFRACTIONr_chiral_restr0.0590.21888
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02114156
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022803
LS refinement shellResolution: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 260 -
Rwork0.251 4827 -
all-5087 -
obs--99.69 %
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)
10.41280.08740.15410.45760.14770.65890.009-0.05130.03130.0742-0.0274-0.0410.0004-0.00090.01840.07340.00080.01850.0762-0.01450.091653.154434.29847.1364
20.8178-0.0196-0.03810.4728-0.02920.4742-0.0023-0.07180.01490.0447-0.0161-0.04770.00340.05170.01840.11080.00530.01410.0593-0.00140.087675.525117.372724.2542
30.65830.14460.00270.49230.04810.6354-0.00630.0534-0.0086-0.0551-0.00610.05450.0015-0.04240.01240.10520.00550.01390.0563-0.00320.106332.10483.7976-8.1363
40.6577-0.00430.22410.3735-0.03020.7287-0.00690.12460.0896-0.05520.00490.0796-0.0757-0.00640.0020.087-0.01360.01940.05970.01560.086643.616826.1747-33.2017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 416
2X-RAY DIFFRACTION2B27 - 416
3X-RAY DIFFRACTION3C27 - 416
4X-RAY DIFFRACTION4D27 - 416

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