HEADER PEPTIDE BINDING PROTEIN 13-AUG-19 6SJQ TITLE 1.7-A RESOLUTION CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF T. TITLE 2 BRUCEI BILBO1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAGELLAR POCKET-RELATED CYTOSKELETAL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 ORGANISM_TAXID: 5691; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BILBO1, UBIQUITIN FOLD, FLAGELLAR POCKET COLLAR, PARASITE, PEPTIDE KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.VIDILASERIS,G.DONG REVDAT 3 19-FEB-20 6SJQ 1 JRNL REVDAT 2 08-JAN-20 6SJQ 1 JRNL REVDAT 1 01-JAN-20 6SJQ 0 JRNL AUTH K.VIDILASERIS,N.LANDREIN,Y.PIVOVAROVA,J.LESIGANG,N.AEKSIRI, JRNL AUTH 2 D.R.ROBINSON,M.BONHIVERS,G.DONG JRNL TITL CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF THE JRNL TITL 2 TRYPANOSOME FLAGELLAR PROTEIN BILBO1 REVEALS A UBIQUITIN JRNL TITL 3 FOLD WITH A LONG STRUCTURED LOOP FOR PROTEIN BINDING. JRNL REF J.BIOL.CHEM. V. 295 1489 2020 JRNL REFN ESSN 1083-351X JRNL PMID 31882537 JRNL DOI 10.1074/JBC.RA119.010768 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.300 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 27060 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2718 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.2700 - 4.2642 1.00 1323 160 0.1470 0.1505 REMARK 3 2 4.2642 - 3.3906 1.00 1357 142 0.1285 0.1522 REMARK 3 3 3.3906 - 2.9637 1.00 1338 150 0.1529 0.2008 REMARK 3 4 2.9637 - 2.6936 1.00 1335 147 0.1574 0.1983 REMARK 3 5 2.6936 - 2.5009 1.00 1343 153 0.1515 0.1594 REMARK 3 6 2.5009 - 2.3538 1.00 1340 148 0.1575 0.1999 REMARK 3 7 2.3538 - 2.2361 1.00 1357 157 0.1521 0.1708 REMARK 3 8 2.2361 - 2.1389 1.00 1316 155 0.1546 0.1977 REMARK 3 9 2.1389 - 2.0566 1.00 1348 144 0.1626 0.2104 REMARK 3 10 2.0566 - 1.9857 1.00 1338 161 0.1612 0.2320 REMARK 3 11 1.9857 - 1.9237 1.00 1367 149 0.1824 0.2170 REMARK 3 12 1.9237 - 1.8687 1.00 1335 143 0.1898 0.2248 REMARK 3 13 1.8687 - 1.8196 1.00 1341 138 0.1983 0.2893 REMARK 3 14 1.8196 - 1.7752 1.00 1348 134 0.2260 0.2584 REMARK 3 15 1.7752 - 1.7349 1.00 1340 166 0.2533 0.2712 REMARK 3 16 1.7349 - 1.6980 0.94 1266 134 0.2516 0.2859 REMARK 3 17 1.6980 - 1.6640 0.84 1118 145 0.2951 0.3122 REMARK 3 18 1.6640 - 1.6327 0.78 1032 98 0.3066 0.3210 REMARK 3 19 1.6327 - 1.6040 0.58 800 94 0.3308 0.3599 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1022 REMARK 3 ANGLE : 1.165 1399 REMARK 3 CHIRALITY : 0.084 149 REMARK 3 PLANARITY : 0.005 185 REMARK 3 DIHEDRAL : 14.488 408 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6SJQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1292103858. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 98166 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 19.279 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THINK PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES NAOH PH 6.5, 30%(W/V) PEG REMARK 280 MME 2000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 25.39650 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 116 REMARK 465 SER A 117 REMARK 465 ALA A 118 REMARK 465 GLY A 119 REMARK 465 GLY A 120 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 399 O HOH A 419 1.89 REMARK 500 O HOH A 432 O HOH A 434 2.01 REMARK 500 O HOH A 328 O HOH A 329 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 69 53.62 39.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2MEK RELATED DB: PDB REMARK 900 NMR STRUCTURE DBREF 6SJQ A 1 120 UNP B2B9C5 B2B9C5_9TRYP 1 120 SEQADV 6SJQ GLY A -2 UNP B2B9C5 EXPRESSION TAG SEQADV 6SJQ SER A -1 UNP B2B9C5 EXPRESSION TAG SEQADV 6SJQ HIS A 0 UNP B2B9C5 EXPRESSION TAG SEQRES 1 A 123 GLY SER HIS MET ALA PHE LEU VAL GLN VAL ALA ALA ASP SEQRES 2 A 123 ILE PHE ASN ASN LYS VAL ASN PHE GLU LEU SER PHE PRO SEQRES 3 A 123 SER ARG PRO SER ILE SER GLU LEU THR ARG SER ALA GLU SEQRES 4 A 123 THR ALA PHE SER ASN GLU ILE SER LEU ARG ARG PRO ASP SEQRES 5 A 123 ASN VAL PRO SER HIS LYS PHE HIS SER SER LYS ILE LYS SEQRES 6 A 123 MET TYR ASP GLU GLU LEU ASN LYS TRP VAL ASP LEU ILE SEQRES 7 A 123 ARG GLU ASP GLN LEU THR ASP TYR CYS GLN LEU TYR VAL SEQRES 8 A 123 PHE GLN PRO PRO ASN GLU TRP HIS LYS GLU SER GLN LYS SEQRES 9 A 123 GLU ILE PRO PRO ALA MET LYS PRO PRO SER SER GLY GLN SEQRES 10 A 123 ARG HIS SER ALA GLY GLY HET GOL A 201 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *135(H2 O) HELIX 1 AA1 SER A 27 ARG A 47 1 21 SHEET 1 AA1 5 ASN A 14 PHE A 22 0 SHEET 2 AA1 5 PHE A 3 ILE A 11 -1 N PHE A 3 O PHE A 22 SHEET 3 AA1 5 CYS A 84 PHE A 89 1 O LEU A 86 N GLN A 6 SHEET 4 AA1 5 LYS A 60 ASP A 65 -1 N LYS A 60 O PHE A 89 SHEET 5 AA1 5 LYS A 70 ASP A 73 -1 O VAL A 72 N MET A 63 SITE 1 AC1 2 ALA A 106 MET A 107 CRYST1 29.713 50.793 37.122 90.00 94.60 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.033655 0.000000 0.002708 0.00000 SCALE2 0.000000 0.019688 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027025 0.00000