HEADER CELL ADHESION 05-SEP-17 5YBJ TITLE STRUCTURE OF APO KANK1 ANKYRIN DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: KN MOTIF AND ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1080-1329; COMPND 5 SYNONYM: ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 15,KIDNEY ANKYRIN COMPND 6 REPEAT-CONTAINING PROTEIN; COMPND 7 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: KANK1, ANKRD15, KANK, KIAA0172; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI-THERMUS THERMOPHILUS SHUTTLE SOURCE 7 VECTOR PTRH1T; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 1085940 KEYWDS CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR Q.GUO,S.LIAO,J.MIN,C.XU,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 4 27-MAR-24 5YBJ 1 REMARK REVDAT 3 24-JAN-18 5YBJ 1 JRNL REVDAT 2 13-DEC-17 5YBJ 1 JRNL SEQRES REVDAT 1 06-DEC-17 5YBJ 0 JRNL AUTH Q.GUO,S.LIAO,Z.ZHU,Y.LI,F.LI,C.XU JRNL TITL STRUCTURAL BASIS FOR THE RECOGNITION OF KINESIN FAMILY JRNL TITL 2 MEMBER 21A (KIF21A) BY THE ANKYRIN DOMAINS OF KANK1 AND JRNL TITL 3 KANK2 PROTEINS. JRNL REF J. BIOL. CHEM. V. 293 557 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29183992 JRNL DOI 10.1074/JBC.M117.817494 REMARK 2 REMARK 2 RESOLUTION. 2.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_2722 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) : 2.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 12362 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.720 REMARK 3 FREE R VALUE TEST SET COUNT : 583 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 44.9995 - 3.7163 0.99 3077 163 0.1958 0.2157 REMARK 3 2 3.7163 - 2.9499 1.00 2953 149 0.2335 0.2664 REMARK 3 3 2.9499 - 2.5771 1.00 2921 131 0.2408 0.2995 REMARK 3 4 2.5771 - 2.3415 0.97 2828 140 0.2232 0.2784 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.460 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 : 0.010 1895 REMARK 3 ANGLE : 1.229 2572 REMARK 3 CHIRALITY : 0.070 302 REMARK 3 PLANARITY : 0.004 336 REMARK 3 DIHEDRAL : 18.645 671 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 5YBJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005005. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12363 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.340 REMARK 200 RESOLUTION RANGE LOW (A) : 44.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, PH 7.5, 0.2M LITHIUM REMARK 280 SULFATE MONOHYDRATE, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 21.45150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.87250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.80100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.87250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.45150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.80100 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12010 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 GLY A 1077 REMARK 465 PHE A 1326 REMARK 465 ALA A 1327 REMARK 465 LYS A 1328 REMARK 465 ALA A 1329 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 HIS A1078 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A1104 CD CE NZ REMARK 470 THR A1107 OG1 CG2 REMARK 470 LYS A1109 CE NZ REMARK 470 ARG A1112 CD NE CZ NH1 NH2 REMARK 470 PHE A1113 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A1129 CG CD CE NZ REMARK 470 LYS A1194 CE NZ REMARK 470 GLU A1209 CG CD OE1 OE2 REMARK 470 GLU A1211 CD OE1 OE2 REMARK 470 GLN A1232 CG CD OE1 NE2 REMARK 470 GLU A1266 CG CD OE1 OE2 REMARK 470 GLU A1310 CG CD OE1 OE2 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 A1101 49.71 -98.55 REMARK 500 ASP A1102 87.53 -152.79 REMARK 500 SER A1130 33.46 -93.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1403 DBREF 5YBJ A 1080 1329 UNP Q14678 KANK1_HUMAN 1080 1329 SEQADV 5YBJ GLY A 1077 UNP Q14678 EXPRESSION TAG SEQADV 5YBJ HIS A 1078 UNP Q14678 EXPRESSION TAG SEQADV 5YBJ MET A 1079 UNP Q14678 EXPRESSION TAG SEQRES 1 A 253 GLY HIS MET ARG GLU ARG TYR GLU LEU SER GLU LYS MET SEQRES 2 A 253 LEU SER ALA CYS ASN LEU LEU LYS ASN THR ILE ASN ASP SEQRES 3 A 253 PRO LYS ALA LEU THR SER LYS ASP MET ARG PHE CYS LEU SEQRES 4 A 253 ASN THR LEU GLN HIS GLU TRP PHE ARG VAL SER SER GLN SEQRES 5 A 253 LYS SER ALA ILE PRO ALA MET VAL GLY ASP TYR ILE ALA SEQRES 6 A 253 ALA PHE GLU ALA ILE SER PRO ASP VAL LEU ARG TYR VAL SEQRES 7 A 253 ILE ASN LEU ALA ASP GLY ASN GLY ASN THR ALA LEU HIS SEQRES 8 A 253 TYR SER VAL SER HIS SER ASN PHE GLU ILE VAL LYS LEU SEQRES 9 A 253 LEU LEU ASP ALA ASP VAL CYS ASN VAL ASP HIS GLN ASN SEQRES 10 A 253 LYS ALA GLY TYR THR PRO ILE MET LEU ALA ALA LEU ALA SEQRES 11 A 253 ALA VAL GLU ALA GLU LYS ASP MET ARG ILE VAL GLU GLU SEQRES 12 A 253 LEU PHE GLY CYS GLY ASP VAL ASN ALA LYS ALA SER GLN SEQRES 13 A 253 ALA GLY GLN THR ALA LEU MET LEU ALA VAL SER HIS GLY SEQRES 14 A 253 ARG ILE ASP MET VAL LYS GLY LEU LEU ALA CYS GLY ALA SEQRES 15 A 253 ASP VAL ASN ILE GLN ASP ASP GLU GLY SER THR ALA LEU SEQRES 16 A 253 MET CYS ALA SER GLU HIS GLY HIS VAL GLU ILE VAL LYS SEQRES 17 A 253 LEU LEU LEU ALA GLN PRO GLY CYS ASN GLY HIS LEU GLU SEQRES 18 A 253 ASP ASN ASP GLY SER THR ALA LEU SER ILE ALA LEU GLU SEQRES 19 A 253 ALA GLY HIS LYS ASP ILE ALA VAL LEU LEU TYR ALA HIS SEQRES 20 A 253 VAL ASN PHE ALA LYS ALA HET GOL A1401 6 HET GOL A1402 6 HET GOL A1403 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 3(C3 H8 O3) FORMUL 5 HOH *15(H2 O) HELIX 1 AA1 SER A 1086 ILE A 1100 1 15 HELIX 2 AA2 ASP A 1102 THR A 1107 1 6 HELIX 3 AA3 SER A 1108 SER A 1127 1 20 HELIX 4 AA4 ILE A 1132 SER A 1147 1 16 HELIX 5 AA5 SER A 1147 ASN A 1156 1 10 HELIX 6 AA6 THR A 1164 HIS A 1172 1 9 HELIX 7 AA7 ASN A 1174 ALA A 1184 1 11 HELIX 8 AA8 THR A 1198 ALA A 1206 1 9 HELIX 9 AA9 ALA A 1210 GLY A 1222 1 13 HELIX 10 AB1 THR A 1236 HIS A 1244 1 9 HELIX 11 AB2 ARG A 1246 CYS A 1256 1 11 HELIX 12 AB3 THR A 1269 GLY A 1278 1 10 HELIX 13 AB4 HIS A 1279 GLN A 1289 1 11 HELIX 14 AB5 THR A 1303 ALA A 1311 1 9 HELIX 15 AB6 HIS A 1313 ASN A 1325 1 13 SITE 1 AC1 3 GLY A1312 LYS A1314 ASP A1315 SITE 1 AC2 3 LEU A1182 ASP A1185 CYS A1187 SITE 1 AC3 7 LYS A1179 LEU A1180 ASP A1183 ALA A1258 SITE 2 AC3 7 ASP A1259 VAL A1260 PRO A1290 CRYST1 42.903 47.602 137.745 90.00 90.00 90.00 P 21 21 21 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 0.023308 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021008 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007260 0.00000