HEADER APOPTOSIS 03-MAR-25 9NLT TITLE CRYSTAL STRUCTURE OF FLPP3-MINIBINDER687 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUF3568 FAMILY PROTEIN; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: MINIBINDER687; COMPND 7 CHAIN: A; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FRANCISELLA TULARENSIS; SOURCE 3 ORGANISM_TAXID: 263; SOURCE 4 GENE: DR87_234; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DE NOVO DESIGN, DEEP LEARNING, PLPP3, MINIBINDER, FRANCISELLA-LIKE KEYWDS 2 LIPOPROTEIN, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,G.GOKCE,A.KANG,G.BHARDWAJ REVDAT 3 07-JAN-26 9NLT 1 JRNL REVDAT 2 05-NOV-25 9NLT 1 JRNL REVDAT 1 22-OCT-25 9NLT 0 JRNL AUTH G.GOKCE-ALPKILIC,B.HUANG,A.LIU,L.S.M.KREUK,Y.WANG,V.ADEBOMI, JRNL AUTH 2 Y.F.BUESO,A.K.BERA,A.KANG,S.R.GERBEN,S.RETTIE,D.K.VAFEADOS, JRNL AUTH 3 N.ROULLIER,I.GORESHNIK,X.LI,D.BAKER,J.J.WOODWARD, JRNL AUTH 4 J.D.MOUGOUS,G.BHARDWAJ JRNL TITL DE NOVO DESIGN OF HIGH-AFFINITY MINIPROTEIN BINDERS JRNL TITL 2 TARGETING FRANCISELLA TULARENSIS VIRULENCE FACTOR. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 64 16058 2025 JRNL REFN ESSN 1521-3773 JRNL PMID 41117072 JRNL DOI 10.1002/ANIE.202516058 REMARK 2 REMARK 2 RESOLUTION. 2.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 2.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 6458 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 647 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 35.9500 - 4.0600 1.00 1251 139 0.1854 0.2246 REMARK 3 2 4.0500 - 3.2200 0.86 1054 118 0.1857 0.2255 REMARK 3 3 3.2200 - 2.8100 1.00 1209 134 0.2302 0.2895 REMARK 3 4 2.8100 - 2.5600 0.90 1098 122 0.2711 0.3298 REMARK 3 5 2.5600 - 2.3700 1.00 1199 134 0.3330 0.3825 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) : 0.341 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.735 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.57 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 1282 REMARK 3 ANGLE : 0.447 1725 REMARK 3 CHIRALITY : 0.040 188 REMARK 3 PLANARITY : 0.003 227 REMARK 3 DIHEDRAL : 15.622 490 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 8.7959 4.0389 16.5261 REMARK 3 T TENSOR REMARK 3 T11: 0.2980 T22: 0.2102 REMARK 3 T33: 0.4154 T12: -0.0073 REMARK 3 T13: -0.1321 T23: -0.0138 REMARK 3 L TENSOR REMARK 3 L11: 3.7625 L22: 3.5402 REMARK 3 L33: 1.0909 L12: 0.0123 REMARK 3 L13: -0.4295 L23: 0.1228 REMARK 3 S TENSOR REMARK 3 S11: 0.1628 S12: 0.5189 S13: -0.4429 REMARK 3 S21: -0.6514 S22: -0.0057 S23: 0.4381 REMARK 3 S31: 0.1562 S32: -0.1436 S33: -0.1159 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 9NLT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1000293641. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : SI(111) DCM REMARK 200 OPTICS : HORIZONTAL PRE-FOCUS BIMORPH REMARK 200 MIRROR & KB BIMORPH MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6471 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.370 REMARK 200 RESOLUTION RANGE LOW (A) : 35.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.32700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 1.47500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS TRIS PROPANE PH 6.5, 0.2 M REMARK 280 SODIUM IODIDE, 20 % W/V PEG 3350 AND 10 % V/V ETHYLENE GLYCOL, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 21.44550 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 ILE B 55 REMARK 465 GLU B 56 REMARK 465 GLY B 57 REMARK 465 ALA B 164 REMARK 465 ASN B 165 REMARK 465 THR B 166 REMARK 465 MET A 1 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 TYR B 60 13.02 -145.40 REMARK 500 ASP B 62 84.88 57.77 REMARK 500 ASN B 70 48.44 -81.83 REMARK 500 SER B 94 19.98 59.49 REMARK 500 ASN B 104 102.55 -172.66 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9NLT B 59 166 UNP A0AAP6R832_FRATU DBREF2 9NLT B A0AAP6R832 30 137 DBREF 9NLT A 1 54 PDB 9NLT 9NLT 1 54 SEQADV 9NLT ILE B 55 UNP A0AAP6R83 EXPRESSION TAG SEQADV 9NLT GLU B 56 UNP A0AAP6R83 EXPRESSION TAG SEQADV 9NLT GLY B 57 UNP A0AAP6R83 EXPRESSION TAG SEQADV 9NLT ARG B 58 UNP A0AAP6R83 EXPRESSION TAG SEQRES 1 B 112 ILE GLU GLY ARG GLN TYR LYS ASP GLY TYR TYR ILE THR SEQRES 2 B 112 THR LEU ASN TYR ASN PHE ASN THR VAL TYR ASN ALA THR SEQRES 3 B 112 LEU GLN ALA ILE GLN ASN GLY GLN THR PHE ASP TYR LYS SEQRES 4 B 112 SER ASN PRO TYR ASP ILE SER VAL ASN LYS ASN ASN GLY SEQRES 5 B 112 THR ASP ALA GLU ILE VAL SER ALA SER ASP SER ASP SER SEQRES 6 B 112 THR ASP SER LEU GLN VAL ALA MET LYS LYS LEU PRO ASN SEQRES 7 B 112 ASN ALA THR ARG ILE SER ILE LYS TYR GLY SER GLN GLY SEQRES 8 B 112 ASN SER ILE ARG SER SER ALA LEU ILE GLY ILE ILE GLU SEQRES 9 B 112 GLY ASN ILE ARG TYR ALA ASN THR SEQRES 1 A 54 MET GLU GLU LYS GLU LYS GLU PHE ASN GLU LYS LEU GLU SEQRES 2 A 54 GLU LEU LYS LYS ALA LYS THR GLU GLU GLU LYS LEU GLU SEQRES 3 A 54 LEU ALA TYR GLU CYS GLY LEU LEU ALA GLY GLU ILE ASN SEQRES 4 A 54 ASP PRO LYS TYR TYR ARG ALA LEU ASP GLU VAL ALA ARG SEQRES 5 A 54 ALA LYS HET IOD B 201 1 HET IOD B 202 1 HETNAM IOD IODIDE ION FORMUL 3 IOD 2(I 1-) FORMUL 5 HOH *11(H2 O) HELIX 1 AA1 ASN B 72 ASN B 86 1 15 HELIX 2 AA2 ASN B 146 TYR B 163 1 18 HELIX 3 AA3 GLU A 3 LYS A 16 1 14 HELIX 4 AA4 THR A 20 ASN A 39 1 20 HELIX 5 AA5 ASP A 40 LYS A 54 1 15 SHEET 1 AA1 5 TYR B 65 LEU B 69 0 SHEET 2 AA1 5 ALA B 134 TYR B 141 -1 O ILE B 139 N TYR B 65 SHEET 3 AA1 5 SER B 122 LEU B 130 -1 N LEU B 130 O ALA B 134 SHEET 4 AA1 5 ASP B 108 ALA B 114 -1 N SER B 113 O LEU B 123 SHEET 5 AA1 5 ASP B 98 ASN B 104 -1 N SER B 100 O VAL B 112 CRYST1 36.166 42.891 54.051 90.00 96.28 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 0.027650 0.000000 0.003040 0.00000 SCALE2 0.000000 0.023315 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018613 0.00000 MASTER 241 0 2 5 5 0 0 6 1279 2 0 14 END