HEADER PROTEIN BINDING 29-MAR-23 8IW5 TITLE CRYSTAL STRUCTURE OF LIPRIN-BETA H2H3 DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPRIN-BETA-1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE F POLYPEPTIDE- COMPND 5 INTERACTING PROTEIN-BINDING PROTEIN 1,PTPRF-INTERACTING PROTEIN- COMPND 6 BINDING PROTEIN 1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PPFIBP1, KIAA1230; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS FOCAL ADHESION, CORTICAL MICROTUBULE STABILIZING COMPLEX, PROTEIN KEYWDS 2 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.ZHANG,S.CHEN,Z.WEI REVDAT 1 08-NOV-23 8IW5 0 JRNL AUTH K.GUO,J.ZHANG,P.HUANG,Y.XU,W.PAN,K.LI,L.CHEN,L.LUO,W.YU, JRNL AUTH 2 S.CHEN,S.HE,Z.WEI,C.YU JRNL TITL KANK1 SHAPES FOCAL ADHESIONS BY ORCHESTRATING PROTEIN JRNL TITL 2 BINDING, MECHANICAL FORCE SENSING, AND PHASE SEPARATION. JRNL REF CELL REP V. 42 13321 2023 JRNL REFN ESSN 2211-1247 JRNL PMID 37874676 JRNL DOI 10.1016/J.CELREP.2023.113321 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 8679 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 445 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 27.3300 - 2.4500 0.82 2455 133 0.2108 0.2548 REMARK 3 2 2.4500 - 1.9500 0.99 2896 160 0.2439 0.2910 REMARK 3 3 1.9500 - 1.7000 0.98 2883 152 0.2230 0.3284 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.410 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 : 0.005 739 REMARK 3 ANGLE : 0.774 1000 REMARK 3 CHIRALITY : 0.043 118 REMARK 3 PLANARITY : 0.005 130 REMARK 3 DIHEDRAL : 14.763 288 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 41 THROUGH 61 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.8452 7.6567 -1.4342 REMARK 3 T TENSOR REMARK 3 T11: 0.2485 T22: 0.2537 REMARK 3 T33: 0.2637 T12: 0.0091 REMARK 3 T13: 0.0092 T23: -0.0398 REMARK 3 L TENSOR REMARK 3 L11: 2.3239 L22: 0.6417 REMARK 3 L33: 0.8002 L12: -0.0430 REMARK 3 L13: 0.5038 L23: 0.4676 REMARK 3 S TENSOR REMARK 3 S11: -0.0356 S12: 0.1545 S13: -0.0352 REMARK 3 S21: -0.3615 S22: 0.0727 S23: 0.1346 REMARK 3 S31: 0.3537 S32: -0.0229 S33: 0.0003 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 62 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.5116 10.1916 11.8484 REMARK 3 T TENSOR REMARK 3 T11: 0.3325 T22: 0.2578 REMARK 3 T33: 0.2357 T12: -0.0243 REMARK 3 T13: -0.0250 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 2.1788 L22: 1.5777 REMARK 3 L33: 2.8055 L12: 1.2869 REMARK 3 L13: -0.7089 L23: 0.8908 REMARK 3 S TENSOR REMARK 3 S11: -0.1672 S12: -0.4019 S13: -0.1199 REMARK 3 S21: 0.2573 S22: 0.2222 S23: -0.1138 REMARK 3 S31: -0.1034 S32: -0.1670 S33: -0.0002 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 45 THROUGH 73 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.9522 15.9277 0.3155 REMARK 3 T TENSOR REMARK 3 T11: 0.2995 T22: 0.2615 REMARK 3 T33: 0.2739 T12: 0.0256 REMARK 3 T13: -0.0142 T23: -0.0193 REMARK 3 L TENSOR REMARK 3 L11: 2.2783 L22: 2.3122 REMARK 3 L33: 2.7271 L12: 1.1813 REMARK 3 L13: -1.8783 L23: -0.6724 REMARK 3 S TENSOR REMARK 3 S11: -0.1654 S12: 0.2542 S13: 0.1345 REMARK 3 S21: -0.1271 S22: 0.0818 S23: -0.0562 REMARK 3 S31: -0.3532 S32: 0.2893 S33: 0.0004 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 74 THROUGH 88 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.4697 4.3726 6.8192 REMARK 3 T TENSOR REMARK 3 T11: 0.2248 T22: 0.2558 REMARK 3 T33: 0.3266 T12: -0.0161 REMARK 3 T13: 0.0219 T23: 0.0186 REMARK 3 L TENSOR REMARK 3 L11: 0.7371 L22: 1.4542 REMARK 3 L33: 5.1662 L12: 0.5360 REMARK 3 L13: 1.2945 L23: 2.6927 REMARK 3 S TENSOR REMARK 3 S11: 0.2674 S12: -0.1543 S13: -0.2086 REMARK 3 S21: 0.2590 S22: 0.0217 S23: -0.0110 REMARK 3 S31: 0.7310 S32: -1.1513 S33: 0.1269 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 8IW5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 04-APR-23. REMARK 100 THE DEPOSITION ID IS D_1300036620. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-21 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 : 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) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8724 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 (%) : 93.3 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 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) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.72400 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M CALCIUM ACETATE, 0.1 M SODIUM REMARK 280 CACODYLATE PH 6.0 AND 25% V/V MPD, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K 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 25.31850 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: 3120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A 39 REMARK 465 PRO A 40 REMARK 465 GLN A 89 REMARK 465 GLY B 39 REMARK 465 PRO B 40 REMARK 465 GLY B 41 REMARK 465 SER B 42 REMARK 465 MET B 43 REMARK 465 GLY B 44 REMARK 465 GLN B 89 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 53 CG CD OE1 OE2 REMARK 470 ASP A 65 CG OD1 OD2 REMARK 470 ASN A 88 CG OD1 ND2 REMARK 470 LEU B 46 CG CD1 CD2 REMARK 470 GLU B 66 CG CD OE1 OE2 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 63 OE1 REMARK 620 2 ASP B 65 OD1 87.5 REMARK 620 3 GLU B 80 OE2 106.3 30.3 REMARK 620 4 GLU B 84 OE2 102.1 33.0 6.9 REMARK 620 5 HOH B 201 O 102.4 29.9 4.3 3.6 REMARK 620 N 1 2 3 4 DBREF 8IW5 A 43 89 UNP Q8C8U0 LIPB1_MOUSE 43 89 DBREF 8IW5 B 43 89 UNP Q8C8U0 LIPB1_MOUSE 43 89 SEQADV 8IW5 GLY A 39 UNP Q8C8U0 EXPRESSION TAG SEQADV 8IW5 PRO A 40 UNP Q8C8U0 EXPRESSION TAG SEQADV 8IW5 GLY A 41 UNP Q8C8U0 EXPRESSION TAG SEQADV 8IW5 SER A 42 UNP Q8C8U0 EXPRESSION TAG SEQADV 8IW5 GLY B 39 UNP Q8C8U0 EXPRESSION TAG SEQADV 8IW5 PRO B 40 UNP Q8C8U0 EXPRESSION TAG SEQADV 8IW5 GLY B 41 UNP Q8C8U0 EXPRESSION TAG SEQADV 8IW5 SER B 42 UNP Q8C8U0 EXPRESSION TAG SEQRES 1 A 51 GLY PRO GLY SER MET GLY SER LEU ARG ALA LEU HIS LEU SEQRES 2 A 51 VAL GLU ASP LEU ARG GLY LEU LEU GLU MET MET GLU THR SEQRES 3 A 51 ASP GLU LYS GLU GLY LEU ARG CYS GLN ILE PRO ASP SER SEQRES 4 A 51 THR ALA GLU VAL LEU ILE GLU TRP LEU GLN ASN GLN SEQRES 1 B 51 GLY PRO GLY SER MET GLY SER LEU ARG ALA LEU HIS LEU SEQRES 2 B 51 VAL GLU ASP LEU ARG GLY LEU LEU GLU MET MET GLU THR SEQRES 3 B 51 ASP GLU LYS GLU GLY LEU ARG CYS GLN ILE PRO ASP SER SEQRES 4 B 51 THR ALA GLU VAL LEU ILE GLU TRP LEU GLN ASN GLN HET CA B 101 1 HETNAM CA CALCIUM ION FORMUL 3 CA CA 2+ FORMUL 4 HOH *39(H2 O) HELIX 1 AA1 SER A 42 MET A 61 1 20 HELIX 2 AA2 GLU A 63 ILE A 74 1 12 HELIX 3 AA3 PRO A 75 GLN A 87 1 13 HELIX 4 AA4 LEU B 46 MET B 61 1 16 HELIX 5 AA5 GLU B 63 GLN B 73 1 11 HELIX 6 AA6 PRO B 75 GLN B 87 1 13 SSBOND 1 CYS A 72 CYS B 72 1555 1656 2.03 LINK OE1 GLU B 63 CA CA B 101 1555 2555 2.52 LINK OD1AASP B 65 CA CA B 101 1555 2555 2.49 LINK OE2AGLU B 80 CA CA B 101 1555 1555 2.41 LINK OE2 GLU B 84 CA CA B 101 1555 1555 2.32 LINK CA CA B 101 O HOH B 201 1555 2545 2.32 CRYST1 29.793 50.637 30.780 90.00 113.44 90.00 P 1 21 1 4 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 0.033565 0.000000 0.014554 0.00000 SCALE2 0.000000 0.019748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035411 0.00000