HEADER CELL ADHESION 21-MAY-20 6X39 TITLE CRYSTAL STRUCTURE OF THE FN5 DOMAIN OF MOUSE 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: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PTPRF, LAR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FIBRONECTIN TYPE III, RECEPTOR PROTEIN TYROSINE PHOSPHATASE, CELL KEYWDS 2 ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR S.BOUYAIN,J.E.KAWAKAMI REVDAT 3 03-APR-24 6X39 1 REMARK REVDAT 2 22-JUN-22 6X39 1 JRNL REVDAT 1 26-MAY-21 6X39 0 JRNL AUTH J.KAWAKAMI,D.BROOKS,R.ZALMAI,S.D.HARTSON,S.BOUYAIN, JRNL AUTH 2 E.R.GEISBRECHT JRNL TITL COMPLEX PROTEIN INTERACTIONS MEDIATE DROSOPHILA LAR FUNCTION JRNL TITL 2 IN MUSCLE TISSUE. JRNL REF PLOS ONE V. 17 69037 2022 JRNL REFN ESSN 1932-6203 JRNL PMID 35622884 JRNL DOI 10.1371/JOURNAL.PONE.0269037 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17_3644 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 13761 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1390 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 28.1900 - 3.6600 1.00 1314 148 0.1717 0.1921 REMARK 3 2 3.6600 - 2.9100 1.00 1265 143 0.1601 0.1768 REMARK 3 3 2.9100 - 2.5400 1.00 1263 142 0.1666 0.1871 REMARK 3 4 2.5400 - 2.3100 1.00 1253 138 0.1547 0.1994 REMARK 3 5 2.3100 - 2.1400 1.00 1250 143 0.1527 0.1860 REMARK 3 6 2.1400 - 2.0200 1.00 1229 135 0.1598 0.1685 REMARK 3 7 2.0200 - 1.9200 0.99 1240 141 0.1509 0.2088 REMARK 3 8 1.9200 - 1.8300 0.98 1209 135 0.1661 0.1977 REMARK 3 9 1.8300 - 1.7600 0.97 1210 138 0.1685 0.2064 REMARK 3 10 1.7600 - 1.7000 0.92 1138 127 0.1900 0.2286 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.144 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.221 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.63 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 : 0.011 779 REMARK 3 ANGLE : 1.155 1062 REMARK 3 CHIRALITY : 0.076 128 REMARK 3 PLANARITY : 0.007 135 REMARK 3 DIHEDRAL : 13.402 286 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 707 THROUGH 809) REMARK 3 ORIGIN FOR THE GROUP (A): 13.4524 47.6506 3.4137 REMARK 3 T TENSOR REMARK 3 T11: 0.0709 T22: 0.1516 REMARK 3 T33: 0.0935 T12: 0.0305 REMARK 3 T13: -0.0208 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.9497 L22: 3.5806 REMARK 3 L33: 1.2652 L12: -0.4896 REMARK 3 L13: -0.2964 L23: 0.6687 REMARK 3 S TENSOR REMARK 3 S11: 0.0751 S12: 0.0323 S13: 0.1016 REMARK 3 S21: 0.0479 S22: -0.1064 S23: -0.0209 REMARK 3 S31: -0.0798 S32: 0.0711 S33: 0.0282 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 6X39 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1000249505. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13907 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 21.30 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.17_3644 REMARK 200 STARTING MODEL: DLAR FN5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM NA-CACODYLATE PH 6.5, 1.4 M NA REMARK 280 -CITRATE TRIBASIC DEHYDRATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 19.56267 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 9.78133 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 9.78133 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 19.56267 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 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 A1116 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 GLY A 704 REMARK 465 PRO A 705 REMARK 465 THR A 706 REMARK 465 ASN A 735 REMARK 465 LYS A 736 REMARK 465 GLN A 737 REMARK 465 ALA A 810 REMARK 465 VAL A 811 REMARK 465 PRO A 812 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 MET A 766 50.95 -91.87 REMARK 500 REMARK 500 REMARK: NULL DBREF 6X39 A 709 812 UNP A2A8L5 PTPRF_MOUSE 709 812 SEQADV 6X39 GLY A 704 UNP A2A8L5 EXPRESSION TAG SEQADV 6X39 PRO A 705 UNP A2A8L5 EXPRESSION TAG SEQADV 6X39 THR A 706 UNP A2A8L5 EXPRESSION TAG SEQADV 6X39 SER A 707 UNP A2A8L5 EXPRESSION TAG SEQADV 6X39 GLY A 708 UNP A2A8L5 EXPRESSION TAG SEQRES 1 A 109 GLY PRO THR SER GLY SER GLY PRO PRO ARG LYS VAL GLU SEQRES 2 A 109 VAL GLU PRO LEU ASN SER THR ALA VAL HIS VAL SER TRP SEQRES 3 A 109 LYS LEU PRO VAL PRO ASN LYS GLN HIS GLY GLN ILE ARG SEQRES 4 A 109 GLY TYR GLN VAL THR TYR VAL ARG LEU GLU ASN GLY GLU SEQRES 5 A 109 PRO ARG GLY GLN PRO ILE ILE GLN ASP VAL MET LEU ALA SEQRES 6 A 109 GLU ALA GLN GLU THR THR ILE SER GLY LEU THR PRO GLU SEQRES 7 A 109 THR THR TYR SER ILE THR VAL ALA ALA TYR THR THR LYS SEQRES 8 A 109 GLY ASP GLY ALA ARG SER LYS PRO LYS VAL VAL THR THR SEQRES 9 A 109 THR GLY ALA VAL PRO HET SOR A 901 26 HETNAM SOR SORBITOL HETSYN SOR D-SORBITOL; D-GLUCITOL FORMUL 2 SOR C6 H14 O6 FORMUL 3 HOH *123(H2 O) SHEET 1 AA1 3 ARG A 713 ASN A 721 0 SHEET 2 AA1 3 ALA A 724 LYS A 730 -1 O HIS A 726 N GLU A 718 SHEET 3 AA1 3 GLU A 772 ILE A 775 -1 O THR A 773 N VAL A 727 SHEET 1 AA2 4 GLU A 755 VAL A 765 0 SHEET 2 AA2 4 ILE A 741 GLU A 752 -1 N TYR A 744 O VAL A 765 SHEET 3 AA2 4 THR A 783 THR A 792 -1 O ALA A 789 N GLN A 745 SHEET 4 AA2 4 LYS A 803 THR A 806 -1 O VAL A 805 N TYR A 784 CRYST1 86.110 86.110 29.344 90.00 90.00 120.00 P 32 2 1 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 0.011613 0.006705 0.000000 0.00000 SCALE2 0.000000 0.013410 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034079 0.00000