HEADER CELL ADHESION 14-DEC-19 6TPT TITLE CRYSTAL STRUCTURES OF FNIII DOMAIN THREE AND FOUR OF THE HUMAN TITLE 2 LEUCOCYTE COMMON ANTIGEN-RELATED PROTEIN, LAR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LEUKOCYTE COMMON ANTIGEN RELATED,LAR; COMPND 5 EC: 3.1.3.48; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PTPRF, LAR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FIBRONECTIN TYPE-III, ADHESION PROTEIN, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR J.P.VILSTRUP,S.S.THIRUP,A.SIMONSEN,T.BIRKEFELDT,D.STRANDBYGAARD REVDAT 2 24-JAN-24 6TPT 1 REMARK REVDAT 1 13-MAY-20 6TPT 0 JRNL AUTH J.VILSTRUP,A.SIMONSEN,T.BIRKEFELDT,D.STRANDBYGARD,J.LYNGSO, JRNL AUTH 2 J.S.PEDERSEN,S.THIRUP JRNL TITL CRYSTAL AND SOLUTION STRUCTURES OF FRAGMENTS OF THE HUMAN JRNL TITL 2 LEUCOCYTE COMMON ANTIGEN-RELATED PROTEIN. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 76 406 2020 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 32355037 JRNL DOI 10.1107/S2059798320003885 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 5225 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 150.2 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 : 0.001 1576 REMARK 3 ANGLE : 0.424 2157 REMARK 3 CHIRALITY : 0.041 237 REMARK 3 PLANARITY : 0.004 283 REMARK 3 DIHEDRAL : 14.589 578 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 6TPT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1292105872. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-18 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 : MAX IV REMARK 200 BEAMLINE : BIOMAX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5225 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 28.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.30 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 : NULL 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: 2EDX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FLUORIDE, 0.1 M BIS-TRIS REMARK 280 PROPANE PH 6.5, AND 20% PEG3350, VAPOR DIFFUSION, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 157.34667 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 78.67333 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 0.00000 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 157.34667 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 78.67333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 157.34667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 78.67333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 157.34667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 78.67333 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 ASP A 706 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 PRO A 536 74.62 -67.98 REMARK 500 SER A 586 -161.60 -107.68 REMARK 500 VAL A 649 -63.68 -120.34 REMARK 500 ARG A 654 57.55 -93.61 REMARK 500 REMARK 500 REMARK: NULL DBREF 6TPT A 512 706 UNP P10586 PTPRF_HUMAN 512 706 SEQRES 1 A 195 PRO ALA GLN PRO ALA ASP PHE GLN ALA GLU VAL GLU SER SEQRES 2 A 195 ASP THR ARG ILE GLN LEU SER TRP LEU LEU PRO PRO GLN SEQRES 3 A 195 GLU ARG ILE ILE MET TYR GLU LEU VAL TYR TRP ALA ALA SEQRES 4 A 195 GLU ASP GLU ASP GLN GLN HIS LYS VAL THR PHE ASP PRO SEQRES 5 A 195 THR SER SER TYR THR LEU GLU ASP LEU LYS PRO ASP THR SEQRES 6 A 195 LEU TYR ARG PHE GLN LEU ALA ALA ARG SER ASP MET GLY SEQRES 7 A 195 VAL GLY VAL PHE THR PRO THR ILE GLU ALA ARG THR ALA SEQRES 8 A 195 GLN SER THR PRO SER ALA PRO PRO GLN LYS VAL MET CYS SEQRES 9 A 195 VAL SER MET GLY SER THR THR VAL ARG VAL SER TRP VAL SEQRES 10 A 195 PRO PRO PRO ALA ASP SER ARG ASN GLY VAL ILE THR GLN SEQRES 11 A 195 TYR SER VAL ALA TYR GLU ALA VAL ASP GLY GLU ASP ARG SEQRES 12 A 195 GLY ARG HIS VAL VAL ASP GLY ILE SER ARG GLU HIS SER SEQRES 13 A 195 SER TRP ASP LEU VAL GLY LEU GLU LYS TRP THR GLU TYR SEQRES 14 A 195 ARG VAL TRP VAL ARG ALA HIS THR ASP VAL GLY PRO GLY SEQRES 15 A 195 PRO GLU SER SER PRO VAL LEU VAL ARG THR ASP GLU ASP HELIX 1 AA1 PRO A 631 ARG A 635 5 5 SHEET 1 AA1 3 GLN A 519 VAL A 522 0 SHEET 2 AA1 3 ILE A 528 SER A 531 -1 O GLN A 529 N GLU A 521 SHEET 3 AA1 3 SER A 566 LEU A 569 -1 O TYR A 567 N LEU A 530 SHEET 1 AA2 4 ASP A 552 PHE A 561 0 SHEET 2 AA2 4 ILE A 540 ALA A 549 -1 N TYR A 547 O HIS A 557 SHEET 3 AA2 4 LEU A 577 SER A 586 -1 O ALA A 583 N GLU A 544 SHEET 4 AA2 4 GLY A 589 VAL A 590 -1 O GLY A 589 N SER A 586 SHEET 1 AA3 4 ASP A 552 PHE A 561 0 SHEET 2 AA3 4 ILE A 540 ALA A 549 -1 N TYR A 547 O HIS A 557 SHEET 3 AA3 4 LEU A 577 SER A 586 -1 O ALA A 583 N GLU A 544 SHEET 4 AA3 4 ILE A 597 ARG A 600 -1 O ILE A 597 N PHE A 580 SHEET 1 AA4 3 GLN A 611 SER A 617 0 SHEET 2 AA4 3 THR A 622 VAL A 628 -1 O SER A 626 N MET A 614 SHEET 3 AA4 3 SER A 668 VAL A 672 -1 O LEU A 671 N VAL A 623 SHEET 1 AA5 4 HIS A 657 SER A 663 0 SHEET 2 AA5 4 GLN A 641 ALA A 648 -1 N TYR A 646 O HIS A 657 SHEET 3 AA5 4 GLU A 679 HIS A 687 -1 O TRP A 683 N ALA A 645 SHEET 4 AA5 4 PRO A 692 GLU A 695 -1 O GLY A 693 N ALA A 686 SHEET 1 AA6 4 HIS A 657 SER A 663 0 SHEET 2 AA6 4 GLN A 641 ALA A 648 -1 N TYR A 646 O HIS A 657 SHEET 3 AA6 4 GLU A 679 HIS A 687 -1 O TRP A 683 N ALA A 645 SHEET 4 AA6 4 VAL A 699 ARG A 702 -1 O VAL A 701 N TYR A 680 CRYST1 63.750 63.750 236.020 90.00 90.00 120.00 P 62 2 2 12 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 0.015686 0.009056 0.000000 0.00000 SCALE2 0.000000 0.018113 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004237 0.00000