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- PDB-4q6k: Crystal structure of a putative neuraminidase (BACCAC_01090) from... -

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Basic information

Entry
Database: PDB / ID: 4q6k
TitleCrystal structure of a putative neuraminidase (BACCAC_01090) from Bacteroides caccae ATCC 43185 at 1.90 A resolution (PSI Community Target)
ComponentsBNR/Asp-box repeat protein
KeywordsHYDROLASE / N-terminal domain of BNR-repeat neuraminidase (PF14873) / BNR repeat-like domain (PF13088) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


exo-alpha-sialidase activity / :
Similarity search - Function
Sialidase, N-terminal / N-terminal domain of BNR-repeat neuraminidase / Immunoglobulin-like - #1290 / Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller ...Sialidase, N-terminal / N-terminal domain of BNR-repeat neuraminidase / Immunoglobulin-like - #1290 / Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / BNR/Asp-box repeat protein
Similarity search - Component
Biological speciesBacteroides caccae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.902 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative neuraminidase (BACCAC_01090) from Bacteroides caccae ATCC 43185 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: BNR/Asp-box repeat protein
B: BNR/Asp-box repeat protein
C: BNR/Asp-box repeat protein
D: BNR/Asp-box repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,81236
Polymers234,8724
Non-polymers1,94032
Water39,5252194
1
A: BNR/Asp-box repeat protein
B: BNR/Asp-box repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,69323
Polymers117,4362
Non-polymers1,25721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint36 kcal/mol
Surface area37370 Å2
MethodPISA
2
C: BNR/Asp-box repeat protein
D: BNR/Asp-box repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,11913
Polymers117,4362
Non-polymers68311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint18 kcal/mol
Surface area37210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.892, 124.337, 107.707
Angle α, β, γ (deg.)90.00, 91.61, 90.00
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
BNR/Asp-box repeat protein / putative neuraminidase


Mass: 58717.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae (bacteria) / Strain: ATCC 43185 / Gene: BACCAC_01090 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A5ZDY0
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2194 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 37-560 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: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.20M potassium citrate, 20.0% polyethylene glycol 3350, 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: 0.91837,0.97939
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 13, 2014 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979391
ReflectionResolution: 1.9→29.778 Å / Num. obs: 196803 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.327 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.970.4131.9624563881996.3
1.97-2.050.2972.6634903935599.3
2.05-2.140.2373.2605643747499.2
2.14-2.250.1814.1615133796499.2
2.25-2.390.154.9629843874599
2.39-2.580.1226649893988798.8
2.58-2.840.0888.1630593855598.4
2.84-3.250.05412.4620213789697
3.25-4.080.03418.6602163673394.9
4.080.02622.6612953705193.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012 BUILT=20131111data scaling
PHENIX1.8.2refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.902→29.778 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.16 / σ(F): 1.31 / Phase error: 15.35 / Stereochemistry target values: MLHL
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED. 7. X-RAY FLUORESCENCE EXCITATION AND WAVELENGTH SCANS, ANOMALOUS DIFFERENCE FOURIERS, AND PRESENCE IN CRYSTALLIZATION CONDITION SUPPORT THE MODELING OF POTASSIUM (K) IONS. 8. RAMACHANDRAN OUTLIER RESIDUES VALINE 464 IS WELL SUPORTED BY ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.1729 9920 5.04 %
Rwork0.1377 186840 -
obs0.1395 196760 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.85 Å2 / Biso mean: 23.323 Å2 / Biso min: 6.87 Å2
Refinement stepCycle: LAST / Resolution: 1.902→29.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16236 0 122 2194 18552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01116992
X-RAY DIFFRACTIONf_angle_d1.28823097
X-RAY DIFFRACTIONf_chiral_restr0.0552614
X-RAY DIFFRACTIONf_plane_restr0.0072974
X-RAY DIFFRACTIONf_dihedral_angle_d12.4436287
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9019-1.92350.24933560.204562216577100
1.9235-1.94610.23672800.191262346514100
1.9461-1.96990.22533290.189162226551100
1.9699-1.99480.21263120.178362466558100
1.9948-2.0210.21693380.167862176555100
2.021-2.04870.20843340.163762516585100
2.0487-2.0780.21123160.164162276543100
2.078-2.1090.19323150.152462586573100
2.109-2.14190.18773120.147662436555100
2.1419-2.1770.17443260.138562676593100
2.177-2.21460.18413790.134461576536100
2.2146-2.25480.17793170.136562836600100
2.2548-2.29820.17693510.131861996550100
2.2982-2.34510.1913410.132762546595100
2.3451-2.3960.17962980.131862726570100
2.396-2.45170.18713470.131262346581100
2.4517-2.5130.16693180.124762396557100
2.513-2.58090.17483520.124662106562100
2.5809-2.65680.17643540.128362526606100
2.6568-2.74250.16553530.1362396592100
2.7425-2.84050.17763450.13361906535100
2.8405-2.95410.18313210.134562516572100
2.9541-3.08840.1873630.140662346597100
3.0884-3.25110.17563040.146262346538100
3.2511-3.45450.17033220.14286218654099
3.4545-3.72070.16883280.13796208653699
3.7207-4.09430.15043370.12536203654099
4.0943-4.68480.12943150.10316183649898
4.6848-5.89480.11343170.10816211652898
5.8948-29.78210.16923400.15876183652397
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)
10.1587-0.028-0.07230.13410.06150.14380.007-0.009-0.0121-0.0071-0.01540.0388-0.0042-0.0369-00.07840.0038-0.01350.09870.01410.08599.397737.756416.2932
20.1607-0.0185-0.0730.24390.04230.10660.0152-0.02890.0062-0.0048-0.006-0.053-0.00640.03830.00020.0793-0.0048-0.01110.09970.00580.08851.585342.858111.6533
30.15190.0374-0.11520.0609-0.02020.2279-0.0188-0.0429-0.0344-0.009-0.0017-0.01930.07590.085-00.13570.0254-0.00880.1158-0.00390.100623.859831.138364.8351
40.3576-0.188-0.11730.14530.06610.21080.0865-0.03360.0832-0.05450.01060.0037-0.01350.01720.13070.1476-0.00670.01210.088-0.02430.1262-2.559464.355169.9717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 38:560)A38 - 560
2X-RAY DIFFRACTION2(chain B and resseq 38:560)B38 - 560
3X-RAY DIFFRACTION3(chain C and resseq 38:560)C38 - 560
4X-RAY DIFFRACTION4(chain D and resseq 38:560)D38 - 560

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