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- PDB-4jx0: Crystal structure of a two domain protein with unknown function (... -

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Basic information

Entry
Database: PDB / ID: 4jx0
TitleCrystal structure of a two domain protein with unknown function (BF3416) from Bacteroides fragilis NCTC 9343 at 2.90 A resolution
Componentshypothetical protein
KeywordsStructural Genomics / Unknown Function / two domains protein / DUF1735 of PF08522 family / F5_F8_type_C of PF00754 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Domain of unknown function DUF1735 / BT_3987-like, N-terminal domain / ntegrin, alpha v. Chain A, domain 3 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BF3416) from Bacteroides fragilis NCTC 9343 at 2.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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
Revision 1.5Oct 9, 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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9367
Polymers73,6442
Non-polymers2915
Water2,684149
1
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0654
Polymers36,8221
Non-polymers2433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8713
Polymers36,8221
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: hypothetical protein
B: hypothetical protein
hetero molecules

A: hypothetical protein
B: hypothetical protein
hetero molecules

A: hypothetical protein
B: hypothetical protein
hetero molecules

A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,74328
Polymers294,5778
Non-polymers1,16620
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area13870 Å2
ΔGint-146 kcal/mol
Surface area112720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.341, 118.742, 239.871
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-401-

MG

21B-401-

MG

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein hypothetical protein


Mass: 36822.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF3416, BF9343_3326, YP_213022.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5L9W9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 25-343 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: 3.88 Å3/Da / Density % sol: 68.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M magnesium chloride, 50.0% polyethylene glycol 200, 0.1M sodium cacodylate pH 6.5, 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: 0.97879
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 2.9→46.829 Å / Num. obs: 25634 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 67.253 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 11.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.9-30.7382.615427233694.7
3-3.120.5533.517738255199.4
3.12-3.260.3755.117332251099.4
3.26-3.440.2477.518103265299.6
3.44-3.650.1959.315763249499.2
3.65-3.930.1511.817272254599.5
3.93-4.320.10315.817957257399.8
4.32-4.940.0819.117479258799.3
4.94-6.190.116.716510258998.7
6.190.07222.317639278198.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.9→46.829 Å / Cor.coef. Fo:Fc: 0.9118 / Cor.coef. Fo:Fc free: 0.8893 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM ...Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS 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. MAD PHASE RESTRAINTS WERE USED DURING REFINEMENT. 7. TETRAETHYLENE GLYCOL (PG4) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 8. MAGNESIUM ION THE CRYSTALLIZATION SOLUTION ARE MODELED. MG-O DISTANCE AND ANGLE RESTRAINTS WERE INCLUDED TO MAINTAIN THE GEOMETRY OF THE MG-6(H2O) CLUSTERS NEAR GLU-144 AND DISTANCE RESTRAINTS WERE USED FOR MG NEAR ASP-234 IN BOTH CHAINS. 9. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (AUTONCS FOLLOWED BY ADDITIONAL MANUAL PRUNING).
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 1299 5.07 %RANDOM
Rwork0.195 ---
obs0.1967 25634 98.95 %-
Displacement parametersBiso max: 133.92 Å2 / Biso mean: 46.9052 Å2 / Biso min: 13.37 Å2
Baniso -1Baniso -2Baniso -3
1--8.6126 Å20 Å20 Å2
2---1.9967 Å20 Å2
3---10.6093 Å2
Refine analyzeLuzzati coordinate error obs: 0.387 Å
Refinement stepCycle: LAST / Resolution: 2.9→46.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4798 0 14 149 4961
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2726SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes138HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1367HARMONIC5
X-RAY DIFFRACTIONt_it9691HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion638SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9839SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9691HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg17540HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion3.01
LS refinement shellResolution: 2.9→3.02 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3076 116 4.24 %
Rwork0.2553 2619 -
all0.2577 2735 -
obs--98.95 %
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)
10.07590.10060.12280.16940.50282.3257-0.00530.08450.08460.00980.0278-0.09370.01610.0593-0.0226-0.07670.0158-0.01220.0105-0.01660.015517.499718.0692142.229
20.35870.03470.13781.2739-0.76350.16510.0193-0.02450.0377-0.0426-0.0984-0.05720.01130.0990.0791-0.01810.02620.06770.01710.0534-0.057716.300735.950178.7652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|42 - A|343 }A42 - 343
2X-RAY DIFFRACTION2{ B|42 - B|343 }B42 - 343

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