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- PDB-3ks7: Crystal structure of Putative Peptide:N-glycosidase F (PNGase F) ... -

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Basic information

Entry
Database: PDB / ID: 3ks7
TitleCrystal structure of Putative Peptide:N-glycosidase F (PNGase F) (YP_210507.1) from Bacteroides fragilis NCTC 9343 at 2.30 A resolution
ComponentsPutative Putative PNGase F
KeywordsHYDROLASE / Putative Peptide:N-glycosidase F (PNGase F) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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
IODIDE ION / N-glycanase_N domain-containing protein
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative Peptide:N-glycosidase F (PNGase F) (YP_210507.1) from Bacteroides fragilis NCTC 9343 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Putative PNGase F
B: Putative Putative PNGase F
C: Putative Putative PNGase F
D: Putative Putative PNGase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,53543
Polymers178,9274
Non-polymers2,60839
Water8,215456
1
A: Putative Putative PNGase F
B: Putative Putative PNGase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,92824
Polymers89,4632
Non-polymers1,46522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-22.9 kcal/mol
Surface area30910 Å2
MethodPISA
2
C: Putative Putative PNGase F
D: Putative Putative PNGase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,60619
Polymers89,4632
Non-polymers1,14317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-22 kcal/mol
Surface area30900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.057, 119.221, 154.314
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A25 - 415
2114B25 - 415
3114C25 - 415
4114D25 - 415
DetailsANALYTICAL SIZE EXCULSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF THE DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
Putative Putative PNGase F


Mass: 44731.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Strain: ATCC 25285 / NCTC 9343 / Gene: BF0811 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LH31
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE: THIS CONSTRUCT (RESIDUE 20-415) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ...SEQUENCE: THIS CONSTRUCT (RESIDUE 20-415) 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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25.0000% polyethylene glycol 3350, 0.2070M ammonium iodide, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97922,0.97876
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979221
30.978761
ReflectionResolution: 2.3→29.881 Å / Num. obs: 87284 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 43.391 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.363.80.78912412563980.78999.9
2.36-2.423.80.7021.12337662270.702100
2.42-2.493.80.5691.32282960710.56999.9
2.49-2.573.80.4861.62208958870.486100
2.57-2.663.80.3732.12157057320.37399.9
2.66-2.753.80.3042.52082655320.304100
2.75-2.853.80.2493.12001453270.249100
2.85-2.973.80.1963.91944051720.196100
2.97-3.13.80.164.71854049340.16100
3.1-3.253.80.1176.41782047460.117100
3.25-3.433.70.0868.51697245330.086100
3.43-3.643.80.06810.21599642600.068100
3.64-3.893.70.06310.81515640460.06399.9
3.89-4.23.70.05910.81396037470.05999.9
4.2-4.63.70.0512.21291934730.0599.8
4.6-5.143.70.04613.61173931550.04699.8
5.14-5.943.70.04913.41032427920.04999.6
5.94-7.273.70.0513.4870723700.0599.6
7.27-10.293.60.04513.6673018620.04599.2
10.29-29.883.40.04111.5348110200.04193.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.881 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 15.772 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.302 / ESU R Free: 0.219
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. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLS MOTION DETERMINATION SERVER. 4. ANOMALOUS DIFFERENCE MAPS SUPPORTED THE MODELING OF IODIDE (IOD) FROM THE CRYSTALLIZATION SOLUTION. THE OCCUPANCIES ON THE IODIDES WERE REDUCED TO ACCOUNT FOR THE OBSERVED SCATTERING. 5. ETHYLENE GLYCOL (EDO) USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE AND CHLORIDE (CL) FROM THE PURIFICATION/ CRYSTALLIZATION SOLUTIONS WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 4375 5 %RANDOM
Rwork0.201 ---
obs0.203 87221 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.28 Å2 / Biso mean: 26.071 Å2 / Biso min: 3.44 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å20 Å2
2---0.86 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12201 0 105 456 12762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212741
X-RAY DIFFRACTIONr_bond_other_d0.0010.028604
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.95717368
X-RAY DIFFRACTIONr_angle_other_deg0.667320958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.82851603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.27723.916572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.251152017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2741580
X-RAY DIFFRACTIONr_chiral_restr0.0610.21913
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114255
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022581
X-RAY DIFFRACTIONr_mcbond_it0.4211.57861
X-RAY DIFFRACTIONr_mcbond_other0.0731.53164
X-RAY DIFFRACTIONr_mcangle_it0.806212777
X-RAY DIFFRACTIONr_scbond_it1.12834880
X-RAY DIFFRACTIONr_scangle_it1.8444.54569
Refine LS restraints NCS

Ens-ID: 1 / Number: 4921 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.230.5
2BMEDIUM POSITIONAL0.280.5
3CMEDIUM POSITIONAL0.240.5
4DMEDIUM POSITIONAL0.250.5
1AMEDIUM THERMAL0.42
2BMEDIUM THERMAL0.392
3CMEDIUM THERMAL0.372
4DMEDIUM THERMAL0.422
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 307 -
Rwork0.339 6081 -
all-6388 -
obs--99.81 %
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)
10.9406-0.0606-0.13891.18290.09981.00910.041-0.0716-0.1070.01750.0283-0.13160.10690.0634-0.06940.0534-0.0098-0.01680.0187-0.01690.095216.0444-74.9396-8.3211
20.74310.2353-0.19531.19360.1160.8989-0.0504-0.0393-0.04290.02510.0954-0.1108-0.0975-0.0005-0.0450.09050.02840.0310.0398-0.01830.039611.6853-41.53474.5055
31.35810.4579-0.21650.96040.11331.05830.07910.17860.04660.0083-0.02540.04380.00940.0352-0.05370.11850.05490.00940.0709-0.02660.053645.3454-80.275935.2713
41.2666-0.06590.05890.81290.20270.8639-0.03660.17440.03720.0470.0393-0.03280.1137-0.1238-0.00260.085-0.07830.00140.1080.0080.012210.2669-80.31842.7981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 415
2X-RAY DIFFRACTION2B26 - 415
3X-RAY DIFFRACTION3C26 - 415
4X-RAY DIFFRACTION4D24 - 415

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