HEADER DE NOVO PROTEIN 08-AUG-23 8Q52 TITLE A PBP-LIKE PROTEIN BUILT FROM FRAGMENTS OF DIFFERENT FOLDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCINE-SPECIFIC-BINDING PROTEIN,CHEMOTAXIS PROTEIN CHEY; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: L-BP,LS-BP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12, THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 83333, 243274; SOURCE 4 STRAIN: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8; SOURCE 5 GENE: LIVK, B3458, JW3423, CHEY, TM_0700; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PROTEIN FOLD EVOLUTION, GENE DUPLICATION, FLAVODOXIN-LIKE FOLD, KEYWDS 2 PERIPLASMIC-BINDING PROTEIN-LIKE I FOLD, SUB-DOMAIN, CHIMERIC KEYWDS 3 PROTEINS, HOMOLOGY, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.SHANMUGARATNAM,S.TOLEDO-PATINO,S.K.GOETZ,J.A.FARIAS-RICO,B.HOCKER REVDAT 2 19-JUN-24 8Q52 1 JRNL REVDAT 1 10-APR-24 8Q52 0 SPRSDE 10-APR-24 8Q52 4QWV JRNL AUTH S.TOLEDO-PATINO,S.K.GOETZ,S.SHANMUGARATNAM,B.HOCKER, JRNL AUTH 2 J.A.FARIAS-RICO JRNL TITL MOLECULAR HANDCRAFT OF A WELL-FOLDED PROTEIN CHIMERA. JRNL REF FEBS LETT. V. 598 1375 2024 JRNL REFN ISSN 0014-5793 JRNL PMID 38508768 JRNL DOI 10.1002/1873-3468.14856 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 20797 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1041 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 41.3600 - 4.1100 1.00 3008 159 0.1585 0.1778 REMARK 3 2 4.1100 - 3.2600 1.00 2857 150 0.1687 0.2471 REMARK 3 3 3.2600 - 2.8500 1.00 2801 148 0.2224 0.2976 REMARK 3 4 2.8500 - 2.5900 1.00 2788 147 0.2308 0.2807 REMARK 3 5 2.5900 - 2.4100 1.00 2786 146 0.2573 0.3352 REMARK 3 6 2.4000 - 2.2600 1.00 2763 145 0.3140 0.3691 REMARK 3 7 2.2600 - 2.1500 0.99 2753 146 0.3476 0.4037 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.346 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.606 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.81 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 : 0.002 2466 REMARK 3 ANGLE : 0.408 3339 REMARK 3 CHIRALITY : 0.043 378 REMARK 3 PLANARITY : 0.003 435 REMARK 3 DIHEDRAL : 3.634 341 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 8Q52 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292132600. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20230630 REMARK 200 DATA SCALING SOFTWARE : XDS 20230630 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20824 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 41.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 25.80 REMARK 200 R MERGE (I) : 0.31300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 26.30 REMARK 200 R MERGE FOR SHELL (I) : 6.08000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.620 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.1M TRIS.HCL, 0.3M LI REMARK 280 SULFATE, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.82000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 64.78000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 64.78000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 10.91000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 64.78000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 64.78000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.73000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 64.78000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.78000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 10.91000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 64.78000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.78000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.73000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 21.82000 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 668 LIES ON A SPECIAL POSITION. 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 MET A 0 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 GLN A 124 53.17 -97.93 REMARK 500 GLN A 139 -169.65 -161.38 REMARK 500 GLN A 222 38.26 -86.17 REMARK 500 ARG A 243 89.29 -66.40 REMARK 500 REMARK 500 REMARK: NULL DBREF 8Q52 A 1 140 UNP P04816 LIVK_ECOLI 24 163 DBREF 8Q52 A 141 241 UNP Q56312 CHEY_THEMA 5 105 DBREF 8Q52 A 242 320 UNP P04816 LIVK_ECOLI 273 351 SEQADV 8Q52 MET A 0 UNP P04816 INITIATING METHIONINE SEQRES 1 A 321 MET ASP ASP ILE LYS VAL ALA VAL VAL GLY ALA MET SER SEQRES 2 A 321 GLY PRO ILE ALA GLN TRP GLY ASP MET GLU PHE ASN GLY SEQRES 3 A 321 ALA ARG GLN ALA ILE LYS ASP ILE ASN ALA LYS GLY GLY SEQRES 4 A 321 ILE LYS GLY ASP LYS LEU VAL GLY VAL GLU TYR ASP ASP SEQRES 5 A 321 ALA CYS ASP PRO LYS GLN ALA VAL ALA VAL ALA ASN LYS SEQRES 6 A 321 ILE VAL ASN ASP GLY ILE LYS TYR VAL ILE GLY HIS LEU SEQRES 7 A 321 CYS SER SER SER THR GLN PRO ALA SER ASP ILE TYR GLU SEQRES 8 A 321 ASP GLU GLY ILE LEU MET ILE SER PRO GLY ALA THR ASN SEQRES 9 A 321 PRO GLU LEU THR GLN ARG GLY TYR GLN HIS ILE MET ARG SEQRES 10 A 321 THR ALA GLY LEU ASP SER SER GLN GLY PRO THR ALA ALA SEQRES 11 A 321 LYS TYR ILE LEU GLU THR VAL LYS PRO GLN ARG VAL LEU SEQRES 12 A 321 ILE VAL ASP ASP ALA ALA PHE MET ARG MET MET LEU LYS SEQRES 13 A 321 ASP ILE ILE THR LYS ALA GLY TYR GLU VAL ALA GLY GLU SEQRES 14 A 321 ALA THR ASN GLY ARG GLU ALA VAL GLU LYS TYR LYS GLU SEQRES 15 A 321 LEU LYS PRO ASP ILE VAL THR MET ASP ILE THR MET PRO SEQRES 16 A 321 GLU MET ASN GLY ILE ASP ALA ILE LYS GLU ILE MET LYS SEQRES 17 A 321 ILE ASP PRO ASN ALA LYS ILE ILE VAL CYS SER ALA MET SEQRES 18 A 321 GLY GLN GLN ALA MET VAL ILE GLU ALA ILE LYS ALA GLY SEQRES 19 A 321 ALA LYS ASP PHE ILE VAL LYS PRO LYS ARG TYR ASP GLN SEQRES 20 A 321 ASP PRO ALA ASN GLN GLY ILE VAL ASP ALA LEU LYS ALA SEQRES 21 A 321 ASP LYS LYS ASP PRO SER GLY PRO TYR VAL TRP ILE THR SEQRES 22 A 321 TYR ALA ALA VAL GLN SER LEU ALA THR ALA LEU GLU ARG SEQRES 23 A 321 THR GLY SER ASP GLU PRO LEU ALA LEU VAL LYS ASP LEU SEQRES 24 A 321 LYS ALA ASN GLY ALA ASN THR VAL ILE GLY PRO LEU ASN SEQRES 25 A 321 TRP ASP GLU LYS GLY ASP LEU LYS GLY HET SO4 A 401 5 HET SO4 A 402 5 HET SO4 A 403 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *168(H2 O) HELIX 1 AA1 ILE A 15 LYS A 36 1 22 HELIX 2 AA2 ASP A 54 GLY A 69 1 16 HELIX 3 AA3 CYS A 78 GLU A 92 1 15 HELIX 4 AA4 ASN A 103 GLN A 108 5 6 HELIX 5 AA5 GLY A 119 SER A 123 5 5 HELIX 6 AA6 THR A 127 VAL A 136 1 10 HELIX 7 AA7 ALA A 147 ALA A 161 1 15 HELIX 8 AA8 ASN A 171 LYS A 183 1 13 HELIX 9 AA9 MET A 193 MET A 196 5 4 HELIX 10 AB1 ASN A 197 ASP A 209 1 13 HELIX 11 AB2 GLN A 222 GLY A 233 1 12 HELIX 12 AB3 ARG A 243 ALA A 249 5 7 HELIX 13 AB4 ASN A 250 ASP A 260 1 11 HELIX 14 AB5 GLY A 266 GLY A 287 1 22 HELIX 15 AB6 GLU A 290 GLY A 302 1 13 SHEET 1 AA1 5 LEU A 44 ASP A 50 0 SHEET 2 AA1 5 ILE A 3 GLY A 9 1 N VAL A 5 O VAL A 45 SHEET 3 AA1 5 TYR A 72 ILE A 74 1 O ILE A 74 N ALA A 6 SHEET 4 AA1 5 LEU A 95 SER A 98 1 O ILE A 97 N VAL A 73 SHEET 5 AA1 5 ILE A 114 ARG A 116 1 O MET A 115 N MET A 96 SHEET 1 AA2 5 GLU A 164 ALA A 169 0 SHEET 2 AA2 5 ARG A 140 VAL A 144 1 N VAL A 141 O GLU A 164 SHEET 3 AA2 5 ILE A 186 ASP A 190 1 O THR A 188 N VAL A 144 SHEET 4 AA2 5 ILE A 214 ALA A 219 1 O ILE A 215 N VAL A 187 SHEET 5 AA2 5 ASP A 236 LYS A 240 1 O LYS A 240 N SER A 218 SHEET 1 AA3 2 ALA A 303 THR A 305 0 SHEET 2 AA3 2 GLY A 308 LEU A 310 -1 O LEU A 310 N ALA A 303 SSBOND 1 CYS A 53 CYS A 78 1555 1555 2.03 CISPEP 1 GLY A 75 HIS A 76 0 -1.21 CRYST1 129.560 129.560 43.640 90.00 90.00 90.00 P 41 21 2 8 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 0.007718 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007718 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022915 0.00000