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- PDB-3nng: Crystal structure of the F5/8 type C domain of Q5LFR2_BACFN prote... -

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Basic information

Entry
Database: PDB / ID: 3nng
TitleCrystal structure of the F5/8 type C domain of Q5LFR2_BACFN protein from Bacteroides fragilis. Northeast Structural Genomics Consortium Target BfR258E
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / F5_F8_type_C domain / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Domain of unknown function DUF1735 / Domain of unknown function (DUF1735) / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Exo-alpha sialidase / F5/8 type C domain-containing protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.177 Å
AuthorsVorobiev, S. / Su, M. / Dimaio, F. / Baker, D. / Seetharaman, J. / Janjua, J. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. ...Vorobiev, S. / Su, M. / Dimaio, F. / Baker, D. / Seetharaman, J. / Janjua, J. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the F5/8 type C domain of Q5LFR2_BACFN protein from Bacteroides fragilis.
Authors: Vorobiev, S. / Su, M. / Dimaio, F. / Baker, D. / Seetharaman, J. / Janjua, J. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / ...Authors: Vorobiev, S. / Su, M. / Dimaio, F. / Baker, D. / Seetharaman, J. / Janjua, J. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: 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_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_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.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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3434
Polymers38,2622
Non-polymers802
Water1,964109
1
A: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1712
Polymers19,1311
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1712
Polymers19,1311
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.208, 62.463, 72.001
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsmonomer,24.72 kD,99.6%

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Components

#1: Protein uncharacterized protein


Mass: 19131.180 Da / Num. of mol.: 2 / Fragment: F5_F8_type_C domain / Mutation: truncation: 1-178; E157V; C-tag: LEHHHHHH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 25285/NCTC 9343 / Gene: BF1314 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q5LFR2, UniProt: A0A380YW85*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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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: 1.68 Å3/Da / Density % sol: 26.83 %
Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 7
Details: 40% PEG 4000, 0.1M calcium chloride, 0.1M Bis-Tris Propane, pH 7.0, Microbatch under Paraffin oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97907 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 15, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.177→50 Å / Num. all: 26092 / Num. obs: 26066 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 21.8
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 5.7 / Num. unique all: 2589 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
Rosettaphasing
CNSphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1k3i

1k3i


Resolution: 2.177→31.232 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.85 / Stereochemistry target values: ML
Details: REMARK 3 TLS DETAILS. REMARK 3 NUMBER OF TLS GROUPS: 2 REMARK 3 ORIGIN: CENTER OF MASS REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: chain A REMARK 3 ORIGIN FOR THE GROUP (A): 53.8893 19.5140 ...Details: REMARK 3 TLS DETAILS. REMARK 3 NUMBER OF TLS GROUPS: 2 REMARK 3 ORIGIN: CENTER OF MASS REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: chain A REMARK 3 ORIGIN FOR THE GROUP (A): 53.8893 19.5140 43.3722 REMARK 3 T TENSOR REMARK 3 T11: 0.0224 T22: 0.0412 REMARK 3 T33: 0.0569 T12: -0.0025 REMARK 3 T13: 0.0007 T23: -0.0048 REMARK 3 L TENSOR REMARK 3 L11: 0.5361 L22: 0.6015 REMARK 3 L33: 0.7865 L12: 0.0493 REMARK 3 L13: -0.1665 L23: -0.4384 REMARK 3 S TENSOR REMARK 3 S11: 0.0156 S12: -0.0111 S13: -0.0154 REMARK 3 S21: 0.0017 S22: -0.0052 S23: 0.0173 REMARK 3 S31: 0.0525 S32: 0.0031 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: chain B REMARK 3 ORIGIN FOR THE GROUP (A): 56.8234 40.9299 28.6750 REMARK 3 T TENSOR REMARK 3 T11: 0.1332 T22: 0.0819 REMARK 3 T33: 0.0760 T12: -0.0212 REMARK 3 T13: -0.0086 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 0.5272 L22: 0.4820 REMARK 3 L33: 0.9895 L12: -0.1375 REMARK 3 L13: 0.1975 L23: -0.1302 REMARK 3 S TENSOR REMARK 3 S11: -0.0430 S12: 0.0281 S13: 0.0095 REMARK 3 S21: -0.0465 S22: -0.0134 S23: 0.0236 REMARK 3 S31: -0.2635 S32: 0.0910 S33: -0.0000
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1296 4.98 %RANDOM
Rwork0.164 ---
obs0.167 26014 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.548 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 92.65 Å2 / Biso mean: 28.961 Å2 / Biso min: 4.98 Å2
Baniso -1Baniso -2Baniso -3
1-6.176 Å20 Å2-0 Å2
2--1.281 Å2-0 Å2
3----7.457 Å2
Refinement stepCycle: LAST / Resolution: 2.177→31.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 2 109 2529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072492
X-RAY DIFFRACTIONf_angle_d1.0263407
X-RAY DIFFRACTIONf_chiral_restr0.074358
X-RAY DIFFRACTIONf_plane_restr0.004441
X-RAY DIFFRACTIONf_dihedral_angle_d18.528854
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.177-2.2640.2751440.1622657280197
2.264-2.3670.2821590.18127542913100
2.367-2.4910.261540.1827822936100
2.491-2.6480.2481300.17527462876100
2.648-2.8520.2341390.18127572896100
2.852-3.1390.2661240.16927712895100
3.139-3.5920.211710.16127242895100
3.592-4.5230.1811350.13927772912100
4.523-31.2350.1841400.14727502890100
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)
10.53610.0493-0.16650.6015-0.43840.78650.0156-0.0111-0.01540.0017-0.00520.01730.05250.003100.0224-0.00250.00070.0412-0.00480.056953.889319.51443.3722
20.5272-0.13750.19750.482-0.13020.9895-0.0430.02810.0095-0.0465-0.01340.0236-0.26350.091-00.1332-0.0212-0.00860.08190.00230.07656.823440.929928.675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA186 - 338
2X-RAY DIFFRACTION2chain BB188 - 338

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