HEADER STRUCTURAL PROTEIN 23-OCT-19 6L5H TITLE CRYSTAL STRUCTURE OF HUMAN ROOTLETIN 1108-1200 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ROOTLETIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CILIARY ROOTLET COILED-COIL PROTEIN; COMPND 5 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: CROCC, KIAA0445; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CENTROSOME, ROOTLETIN, COILED-COIL, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.KIM,H.J.CHOI REVDAT 1 29-JUL-20 6L5H 0 JRNL AUTH D.KO,J.KIM,K.RHEE,H.J.CHOI JRNL TITL IDENTIFICATION OF A STRUCTURALLY DYNAMIC DOMAIN FOR OLIGOMER JRNL TITL 2 FORMATION IN ROOTLETIN. JRNL REF J.MOL.BIOL. V. 432 3915 2020 JRNL REFN ESSN 1089-8638 JRNL PMID 32325071 JRNL DOI 10.1016/J.JMB.2020.04.012 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16-3549 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 40057 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 1906 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 22.0870 - 3.1316 0.98 2808 147 0.1952 0.2082 REMARK 3 2 3.1316 - 2.4867 1.00 2764 140 0.1992 0.2372 REMARK 3 3 2.4867 - 2.1727 1.00 2751 143 0.1754 0.1782 REMARK 3 4 2.1727 - 1.9742 1.00 2787 124 0.1806 0.2104 REMARK 3 5 1.9742 - 1.8327 1.00 2731 130 0.1824 0.1683 REMARK 3 6 1.8327 - 1.7247 1.00 2769 131 0.1686 0.1938 REMARK 3 7 1.7247 - 1.6384 1.00 2707 158 0.1689 0.1590 REMARK 3 8 1.6384 - 1.5671 1.00 2739 120 0.1615 0.1756 REMARK 3 9 1.5671 - 1.5068 0.99 2710 143 0.1667 0.1929 REMARK 3 10 1.5068 - 1.4548 0.96 2578 135 0.1989 0.2022 REMARK 3 11 1.4548 - 1.4093 1.00 2720 145 0.2177 0.2381 REMARK 3 12 1.4093 - 1.3690 1.00 2703 134 0.2197 0.2275 REMARK 3 13 1.3690 - 1.3330 1.00 2751 119 0.2216 0.2231 REMARK 3 14 1.3330 - 1.3005 0.97 2633 137 0.2592 0.2538 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.90 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6L5H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1300014224. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40235 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.53100 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.0, 14% PEG 4000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 69.54400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.08100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 69.54400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.08100 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 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 1104 REMARK 465 ALA A 1105 REMARK 465 GLN A 1188 REMARK 465 GLU A 1189 REMARK 465 GLY A 1190 REMARK 465 ARG A 1191 REMARK 465 GLU A 1192 REMARK 465 VAL A 1193 REMARK 465 GLN A 1194 REMARK 465 ARG A 1195 REMARK 465 GLN A 1196 REMARK 465 GLU A 1197 REMARK 465 ALA A 1198 REMARK 465 GLY A 1199 REMARK 465 GLU A 1200 REMARK 465 TRP A 1201 REMARK 465 GLY B 1104 REMARK 465 ALA B 1105 REMARK 465 GLN B 1188 REMARK 465 GLU B 1189 REMARK 465 GLY B 1190 REMARK 465 ARG B 1191 REMARK 465 GLU B 1192 REMARK 465 VAL B 1193 REMARK 465 GLN B 1194 REMARK 465 ARG B 1195 REMARK 465 GLN B 1196 REMARK 465 GLU B 1197 REMARK 465 ALA B 1198 REMARK 465 GLY B 1199 REMARK 465 GLU B 1200 REMARK 465 TRP B 1201 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU B 1157 O HOH B 1301 2.19 REMARK 500 OE2 GLU A 1167 O HOH A 1301 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1388 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A1389 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A1390 DISTANCE = 8.23 ANGSTROMS REMARK 525 HOH B1393 DISTANCE = 6.03 ANGSTROMS DBREF 6L5H A 1108 1200 UNP Q5TZA2 CROCC_HUMAN 1108 1200 DBREF 6L5H B 1108 1200 UNP Q5TZA2 CROCC_HUMAN 1108 1200 SEQADV 6L5H GLY A 1104 UNP Q5TZA2 EXPRESSION TAG SEQADV 6L5H ALA A 1105 UNP Q5TZA2 EXPRESSION TAG SEQADV 6L5H MSE A 1106 UNP Q5TZA2 EXPRESSION TAG SEQADV 6L5H GLU A 1107 UNP Q5TZA2 EXPRESSION TAG SEQADV 6L5H TRP A 1201 UNP Q5TZA2 EXPRESSION TAG SEQADV 6L5H GLY B 1104 UNP Q5TZA2 EXPRESSION TAG SEQADV 6L5H ALA B 1105 UNP Q5TZA2 EXPRESSION TAG SEQADV 6L5H MSE B 1106 UNP Q5TZA2 EXPRESSION TAG SEQADV 6L5H GLU B 1107 UNP Q5TZA2 EXPRESSION TAG SEQADV 6L5H TRP B 1201 UNP Q5TZA2 EXPRESSION TAG SEQRES 1 A 98 GLY ALA MSE GLU SER THR VAL ASN ALA LEU THR SER GLU SEQRES 2 A 98 LEU ARG ASP LEU ARG ALA GLN ARG GLU GLU ALA ALA ALA SEQRES 3 A 98 ALA HIS ALA GLN GLU VAL ARG ARG LEU GLN GLU GLN ALA SEQRES 4 A 98 ARG ASP LEU GLY LYS GLN ARG ASP SER CYS LEU ARG GLU SEQRES 5 A 98 ALA GLU GLU LEU ARG THR GLN LEU ARG LEU LEU GLU ASP SEQRES 6 A 98 ALA ARG ASP GLY LEU ARG ARG GLU LEU LEU GLU ALA GLN SEQRES 7 A 98 ARG LYS LEU ARG GLU SER GLN GLU GLY ARG GLU VAL GLN SEQRES 8 A 98 ARG GLN GLU ALA GLY GLU TRP SEQRES 1 B 98 GLY ALA MSE GLU SER THR VAL ASN ALA LEU THR SER GLU SEQRES 2 B 98 LEU ARG ASP LEU ARG ALA GLN ARG GLU GLU ALA ALA ALA SEQRES 3 B 98 ALA HIS ALA GLN GLU VAL ARG ARG LEU GLN GLU GLN ALA SEQRES 4 B 98 ARG ASP LEU GLY LYS GLN ARG ASP SER CYS LEU ARG GLU SEQRES 5 B 98 ALA GLU GLU LEU ARG THR GLN LEU ARG LEU LEU GLU ASP SEQRES 6 B 98 ALA ARG ASP GLY LEU ARG ARG GLU LEU LEU GLU ALA GLN SEQRES 7 B 98 ARG LYS LEU ARG GLU SER GLN GLU GLY ARG GLU VAL GLN SEQRES 8 B 98 ARG GLN GLU ALA GLY GLU TRP HET MSE A1106 8 HET MSE B1106 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 3 HOH *183(H2 O) HELIX 1 AA1 MSE A 1106 SER A 1187 1 82 HELIX 2 AA2 GLU B 1107 SER B 1187 1 81 SSBOND 1 CYS A 1152 CYS B 1152 1555 1555 2.06 LINK C MSE A1106 N GLU A1107 1555 1555 1.33 LINK C MSE B1106 N GLU B1107 1555 1555 1.34 CRYST1 139.088 32.162 36.997 90.00 96.17 90.00 C 1 2 1 8 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 0.007190 0.000000 0.000777 0.00000 SCALE2 0.000000 0.031093 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027186 0.00000 HETATM 1 N MSE A1106 -56.046 8.656 21.900 1.00 54.41 N HETATM 2 CA MSE A1106 -56.402 9.186 20.587 1.00 56.29 C HETATM 3 C MSE A1106 -55.612 8.531 19.458 1.00 69.02 C HETATM 4 O MSE A1106 -54.479 8.085 19.645 1.00 60.26 O HETATM 5 CB MSE A1106 -56.187 10.702 20.541 1.00 55.86 C HETATM 6 CG MSE A1106 -57.388 11.523 20.980 1.00 66.85 C HETATM 7 SE MSE A1106 -58.990 11.136 19.932 1.00202.17 SE HETATM 8 CE MSE A1106 -58.307 11.525 18.148 1.00 45.40 C