HEADER STRUCTURAL PROTEIN 25-JUL-25 9W18 TITLE CRYSTAL STRUCTURE OF FN3(6847): A THERMALLY ENHANCED FN3 VARIANT TITLE 2 DESIGNED USING AI AND SCREENED VIA THERMALFOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBRONECTIN3-6847; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS FN3, COMPUTATIONAL DESIGNED, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.ZHENG,S.WANG,P.ZHENG REVDAT 1 10-JUN-26 9W18 0 JRNL AUTH B.ZHENG,S.WANG,P.ZHENG JRNL TITL PREDICTING TEMPERATURE-DEPENDENT PROTEIN STRUCTURE BY JRNL TITL 2 THERMALFOLD JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.44 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 17590 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 885 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 21.8500 - 2.6200 1.00 3060 163 0.1545 0.1694 REMARK 3 2 2.6200 - 2.0800 1.00 3008 158 0.1624 0.2039 REMARK 3 3 2.0800 - 1.8100 1.00 2979 156 0.1593 0.1602 REMARK 3 4 1.8100 - 1.6500 1.00 2968 155 0.1827 0.2009 REMARK 3 5 1.6500 - 1.5300 0.92 2727 145 0.1897 0.2533 REMARK 3 6 1.5300 - 1.4400 0.67 1963 108 0.2206 0.2773 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 806 REMARK 3 ANGLE : 0.890 1092 REMARK 3 CHIRALITY : 0.079 116 REMARK 3 PLANARITY : 0.011 138 REMARK 3 DIHEDRAL : 14.307 288 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): -21.7021 -17.6692 0.5418 REMARK 3 T TENSOR REMARK 3 T11: 0.0778 T22: 0.0579 REMARK 3 T33: 0.0484 T12: -0.0083 REMARK 3 T13: -0.0044 T23: 0.0076 REMARK 3 L TENSOR REMARK 3 L11: 1.7070 L22: 1.8199 REMARK 3 L33: 1.2765 L12: -1.2380 REMARK 3 L13: -0.5799 L23: 0.8302 REMARK 3 S TENSOR REMARK 3 S11: 0.0100 S12: 0.0108 S13: 0.0394 REMARK 3 S21: 0.0537 S22: 0.0177 S23: -0.0430 REMARK 3 S31: 0.0174 S32: 0.0413 S33: -0.0244 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 9W18 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 31-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1300062036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17590 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 22.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 14.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.1 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 : 1.800 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 (%): 50.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4%PEG400, 0.1M_NAOAC-HOAC_PH6.0, REMARK 280 EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 10.50333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.00667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 15.75500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 26.25833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 5.25167 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: 120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 MET A -2 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 80 58.81 -166.67 REMARK 500 REMARK 500 REMARK: NULL DBREF 9W18 A -2 96 PDB 9W18 9W18 -2 96 SEQRES 1 A 99 MET GLY SER SER LYS THR PRO SER ASN LEU ARG VAL VAL SEQRES 2 A 99 SER SER THR ASP THR SER ALA THR ILE ALA TRP ASP ALA SEQRES 3 A 99 PRO PRO TYR PRO VAL ARG TYR TYR ARG ILE SER TYR ARG SEQRES 4 A 99 PRO ALA GLY SER GLY GLY PRO ALA GLN SER PHE THR VAL SEQRES 5 A 99 PRO GLY SER VAL THR THR ALA THR ILE ASP GLY LEU THR SEQRES 6 A 99 PRO GLY THR ASP TYR GLU ILE SER VAL LYS ALA VAL TYR SEQRES 7 A 99 GLY ARG GLY ASP ASN PRO GLU GLU SER GLU PRO VAL SER SEQRES 8 A 99 ILE VAL TRP ASP ARG GLY THR HIS HET EDO A 901 10 HET PEG A 902 17 HET PEG A 903 17 HET PEG A 904 17 HET PEG A 905 17 HET PEG A 906 17 HET SO4 A 907 5 HET SO4 A 908 5 HET SO4 A 909 5 HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM SO4 SULFATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 PEG 5(C4 H10 O3) FORMUL 8 SO4 3(O4 S 2-) FORMUL 11 HOH *95(H2 O) SHEET 1 AA1 3 SER A 5 THR A 13 0 SHEET 2 AA1 3 SER A 16 ASP A 22 -1 O ASP A 22 N SER A 5 SHEET 3 AA1 3 THR A 55 ILE A 58 -1 O ILE A 58 N ALA A 17 SHEET 1 AA2 4 GLN A 45 PRO A 50 0 SHEET 2 AA2 4 TYR A 30 PRO A 37 -1 N ILE A 33 O PHE A 47 SHEET 3 AA2 4 TYR A 67 TYR A 75 -1 O GLU A 68 N ARG A 36 SHEET 4 AA2 4 GLU A 82 GLU A 83 -1 O GLU A 82 N TYR A 75 SHEET 1 AA3 4 GLN A 45 PRO A 50 0 SHEET 2 AA3 4 TYR A 30 PRO A 37 -1 N ILE A 33 O PHE A 47 SHEET 3 AA3 4 TYR A 67 TYR A 75 -1 O GLU A 68 N ARG A 36 SHEET 4 AA3 4 VAL A 87 TRP A 91 -1 O TRP A 91 N TYR A 67 CRYST1 75.680 75.680 31.510 90.00 90.00 120.00 P 61 6 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 0.013214 0.007629 0.000000 0.00000 SCALE2 0.000000 0.015258 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031736 0.00000 CONECT 1405 1406 1407 1409 1410 CONECT 1406 1405 1411 CONECT 1407 1405 1408 1412 1413 CONECT 1408 1407 1414 CONECT 1409 1405 CONECT 1410 1405 CONECT 1411 1406 CONECT 1412 1407 CONECT 1413 1407 CONECT 1414 1408 CONECT 1415 1416 1417 1422 1423 CONECT 1416 1415 1424 CONECT 1417 1415 1418 1425 1426 CONECT 1418 1417 1419 CONECT 1419 1418 1420 1427 1428 CONECT 1420 1419 1421 1429 1430 CONECT 1421 1420 1431 CONECT 1422 1415 CONECT 1423 1415 CONECT 1424 1416 CONECT 1425 1417 CONECT 1426 1417 CONECT 1427 1419 CONECT 1428 1419 CONECT 1429 1420 CONECT 1430 1420 CONECT 1431 1421 CONECT 1432 1433 1434 1439 1440 CONECT 1433 1432 1441 CONECT 1434 1432 1435 1442 1443 CONECT 1435 1434 1436 CONECT 1436 1435 1437 1444 1445 CONECT 1437 1436 1438 1446 1447 CONECT 1438 1437 1448 CONECT 1439 1432 CONECT 1440 1432 CONECT 1441 1433 CONECT 1442 1434 CONECT 1443 1434 CONECT 1444 1436 CONECT 1445 1436 CONECT 1446 1437 CONECT 1447 1437 CONECT 1448 1438 CONECT 1449 1450 1451 1456 1457 CONECT 1450 1449 1458 CONECT 1451 1449 1452 1459 1460 CONECT 1452 1451 1453 CONECT 1453 1452 1454 1461 1462 CONECT 1454 1453 1455 1463 1464 CONECT 1455 1454 1465 CONECT 1456 1449 CONECT 1457 1449 CONECT 1458 1450 CONECT 1459 1451 CONECT 1460 1451 CONECT 1461 1453 CONECT 1462 1453 CONECT 1463 1454 CONECT 1464 1454 CONECT 1465 1455 CONECT 1466 1467 1468 1473 1474 CONECT 1467 1466 1475 CONECT 1468 1466 1469 1476 1477 CONECT 1469 1468 1470 CONECT 1470 1469 1471 1478 1479 CONECT 1471 1470 1472 1480 1481 CONECT 1472 1471 1482 CONECT 1473 1466 CONECT 1474 1466 CONECT 1475 1467 CONECT 1476 1468 CONECT 1477 1468 CONECT 1478 1470 CONECT 1479 1470 CONECT 1480 1471 CONECT 1481 1471 CONECT 1482 1472 CONECT 1483 1484 1485 1490 1491 CONECT 1484 1483 1492 CONECT 1485 1483 1486 1493 1494 CONECT 1486 1485 1487 CONECT 1487 1486 1488 1495 1496 CONECT 1488 1487 1489 1497 1498 CONECT 1489 1488 1499 CONECT 1490 1483 CONECT 1491 1483 CONECT 1492 1484 CONECT 1493 1485 CONECT 1494 1485 CONECT 1495 1487 CONECT 1496 1487 CONECT 1497 1488 CONECT 1498 1488 CONECT 1499 1489 CONECT 1500 1501 1502 1503 1504 CONECT 1501 1500 CONECT 1502 1500 CONECT 1503 1500 CONECT 1504 1500 CONECT 1505 1506 1507 1508 1509 CONECT 1506 1505 CONECT 1507 1505 CONECT 1508 1505 CONECT 1509 1505 CONECT 1510 1511 1512 1513 1514 CONECT 1511 1510 CONECT 1512 1510 CONECT 1513 1510 CONECT 1514 1510 MASTER 246 0 9 0 11 0 0 6 882 1 110 8 END