HEADER LIGASE 10-SEP-25 9SNG TITLE CTLH-CRA DOMAIN OF MURINE RANBP10 MUTANT Q519G, F543L, Y548F AND V556F COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAN-BINDING PROTEIN 10; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RANBP10; COMPND 5 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: RANBP10, KIAA1464; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS (DE3)-RIL KEYWDS CTLH COMPLEX, GID COMPLEX, E3 LIGASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR P.M.VAN GEN HASSEND,H.SCHINDELIN REVDAT 1 18-FEB-26 9SNG 0 JRNL AUTH P.M.VAN GEN HASSEND,H.SCHINDELIN JRNL TITL ENGINEERING CTLH-CRA DOMAINS WITH SWAPPED BINDING JRNL TITL 2 SPECIFICITY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.0 REMARK 3 NUMBER OF REFLECTIONS : 23140 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1128 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 43.0400 - 3.4700 0.99 3602 190 0.1835 0.2143 REMARK 3 2 3.4700 - 2.7600 1.00 3437 217 0.1995 0.2473 REMARK 3 3 2.7600 - 2.4100 1.00 3452 161 0.1964 0.2412 REMARK 3 4 2.4100 - 2.1900 0.86 2947 141 0.2330 0.2703 REMARK 3 5 2.1900 - 2.0300 1.00 3425 167 0.2257 0.2517 REMARK 3 6 2.0300 - 1.9100 0.90 3057 148 0.2877 0.3262 REMARK 3 7 1.9100 - 1.8200 0.54 1847 96 0.3049 0.3432 REMARK 3 8 1.8200 - 1.7400 0.07 245 8 0.3415 0.5044 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.217 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.687 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.40 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 : 0.006 2212 REMARK 3 ANGLE : 0.725 2984 REMARK 3 CHIRALITY : 0.037 332 REMARK 3 PLANARITY : 0.006 397 REMARK 3 DIHEDRAL : 13.950 843 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 8 THROUGH 151) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9830 6.4990 12.3820 REMARK 3 T TENSOR REMARK 3 T11: 0.0960 T22: 0.1577 REMARK 3 T33: 0.0961 T12: 0.0005 REMARK 3 T13: 0.0058 T23: -0.0082 REMARK 3 L TENSOR REMARK 3 L11: 2.3961 L22: 0.8974 REMARK 3 L33: 1.0872 L12: -0.4411 REMARK 3 L13: -0.5791 L23: -0.5139 REMARK 3 S TENSOR REMARK 3 S11: -0.0952 S12: -0.2071 S13: -0.0093 REMARK 3 S21: 0.1182 S22: 0.1033 S23: 0.0476 REMARK 3 S31: -0.0264 S32: -0.1312 S33: 0.0105 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 9 THROUGH 152) REMARK 3 ORIGIN FOR THE GROUP (A): 40.6613 17.9403 3.0828 REMARK 3 T TENSOR REMARK 3 T11: 0.1085 T22: 0.1387 REMARK 3 T33: 0.1260 T12: 0.0077 REMARK 3 T13: -0.0009 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 2.9322 L22: 1.5365 REMARK 3 L33: 0.8123 L12: 0.2611 REMARK 3 L13: 0.4906 L23: -0.3133 REMARK 3 S TENSOR REMARK 3 S11: -0.0571 S12: 0.1275 S13: 0.2978 REMARK 3 S21: -0.0436 S22: -0.0092 S23: -0.0203 REMARK 3 S31: -0.1537 S32: 0.0356 S33: 0.0311 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 9SNG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1292150705. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-SEP-24 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 : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X CDTE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23475 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.737 REMARK 200 RESOLUTION RANGE LOW (A) : 43.042 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : 0.15300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.97900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BISTRIS 6.5, 30% PEG 400, PH REMARK 280 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.31450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.22650 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.31450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.22650 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: 1890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 5 REMARK 465 PRO A 6 REMARK 465 GLU A 7 REMARK 465 SER A 72 REMARK 465 SER A 73 REMARK 465 GLY A 74 REMARK 465 GLY A 75 REMARK 465 GLN A 152 REMARK 465 GLY B 5 REMARK 465 PRO B 6 REMARK 465 GLU B 7 REMARK 465 GLU B 8 REMARK 465 GLU B 67 REMARK 465 VAL B 68 REMARK 465 ARG B 69 REMARK 465 SER B 70 REMARK 465 LEU B 71 REMARK 465 SER B 72 REMARK 465 SER B 73 REMARK 465 GLY B 74 REMARK 465 GLY B 75 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 A 284 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A 285 DISTANCE = 6.00 ANGSTROMS DBREF 9SNG A 7 73 UNP Q6VN19 RBP10_MOUSE 287 353 DBREF 9SNG A 74 152 UNP Q6VN19 RBP10_MOUSE 502 580 DBREF 9SNG B 7 73 UNP Q6VN19 RBP10_MOUSE 287 353 DBREF 9SNG B 74 152 UNP Q6VN19 RBP10_MOUSE 502 580 SEQADV 9SNG GLY A 5 UNP Q6VN19 EXPRESSION TAG SEQADV 9SNG PRO A 6 UNP Q6VN19 EXPRESSION TAG SEQADV 9SNG GLY A 91 UNP Q6VN19 GLN 519 ENGINEERED MUTATION SEQADV 9SNG LEU A 115 UNP Q6VN19 PHE 543 ENGINEERED MUTATION SEQADV 9SNG PHE A 120 UNP Q6VN19 TYR 548 ENGINEERED MUTATION SEQADV 9SNG PHE A 128 UNP Q6VN19 VAL 556 ENGINEERED MUTATION SEQADV 9SNG GLY B 5 UNP Q6VN19 EXPRESSION TAG SEQADV 9SNG PRO B 6 UNP Q6VN19 EXPRESSION TAG SEQADV 9SNG GLY B 91 UNP Q6VN19 GLN 519 ENGINEERED MUTATION SEQADV 9SNG LEU B 115 UNP Q6VN19 PHE 543 ENGINEERED MUTATION SEQADV 9SNG PHE B 120 UNP Q6VN19 TYR 548 ENGINEERED MUTATION SEQADV 9SNG PHE B 128 UNP Q6VN19 VAL 556 ENGINEERED MUTATION SEQRES 1 A 148 GLY PRO GLU GLU GLN ALA SER ILE LYS ASN ARG GLN LYS SEQRES 2 A 148 ILE GLN LYS LEU VAL LEU GLU GLY ARG VAL GLY GLU ALA SEQRES 3 A 148 ILE GLU THR THR GLN ARG PHE TYR PRO GLY LEU LEU GLU SEQRES 4 A 148 HIS ASN PRO ASN LEU LEU PHE MET LEU LYS CYS ARG GLN SEQRES 5 A 148 PHE VAL GLU MET VAL ASN GLY THR ASP SER GLU VAL ARG SEQRES 6 A 148 SER LEU SER SER GLY GLY ASN GLN ALA ALA THR GLU ARG SEQRES 7 A 148 ILE ILE LEU PHE GLY ARG GLU LEU GLY ALA LEU SER GLU SEQRES 8 A 148 GLN LEU GLY ARG GLU TYR GLY LYS ASN LEU ALA HIS THR SEQRES 9 A 148 GLU MET LEU GLN ASP ALA LEU SER LEU LEU ALA PHE SER SEQRES 10 A 148 ASP PRO TRP SER CYS PRO PHE GLY HIS GLN LEU ASP PRO SEQRES 11 A 148 ILE GLN ARG GLU PRO VAL CYS ALA ALA LEU ASN SER ALA SEQRES 12 A 148 ILE LEU GLU SER GLN SEQRES 1 B 148 GLY PRO GLU GLU GLN ALA SER ILE LYS ASN ARG GLN LYS SEQRES 2 B 148 ILE GLN LYS LEU VAL LEU GLU GLY ARG VAL GLY GLU ALA SEQRES 3 B 148 ILE GLU THR THR GLN ARG PHE TYR PRO GLY LEU LEU GLU SEQRES 4 B 148 HIS ASN PRO ASN LEU LEU PHE MET LEU LYS CYS ARG GLN SEQRES 5 B 148 PHE VAL GLU MET VAL ASN GLY THR ASP SER GLU VAL ARG SEQRES 6 B 148 SER LEU SER SER GLY GLY ASN GLN ALA ALA THR GLU ARG SEQRES 7 B 148 ILE ILE LEU PHE GLY ARG GLU LEU GLY ALA LEU SER GLU SEQRES 8 B 148 GLN LEU GLY ARG GLU TYR GLY LYS ASN LEU ALA HIS THR SEQRES 9 B 148 GLU MET LEU GLN ASP ALA LEU SER LEU LEU ALA PHE SER SEQRES 10 B 148 ASP PRO TRP SER CYS PRO PHE GLY HIS GLN LEU ASP PRO SEQRES 11 B 148 ILE GLN ARG GLU PRO VAL CYS ALA ALA LEU ASN SER ALA SEQRES 12 B 148 ILE LEU GLU SER GLN FORMUL 3 HOH *164(H2 O) HELIX 1 AA1 GLU A 8 GLU A 24 1 17 HELIX 2 AA2 ARG A 26 TYR A 38 1 13 HELIX 3 AA3 LEU A 41 HIS A 44 5 4 HELIX 4 AA4 ASN A 45 ASN A 62 1 18 HELIX 5 AA5 ASP A 65 SER A 70 1 6 HELIX 6 AA6 GLN A 77 TYR A 101 1 25 HELIX 7 AA7 HIS A 107 SER A 116 1 10 HELIX 8 AA8 LEU A 117 PHE A 120 5 4 HELIX 9 AA9 ASP A 122 CYS A 126 5 5 HELIX 10 AB1 PHE A 128 GLN A 136 5 9 HELIX 11 AB2 ARG A 137 SER A 151 1 15 HELIX 12 AB3 ALA B 10 GLU B 24 1 15 HELIX 13 AB4 ARG B 26 TYR B 38 1 13 HELIX 14 AB5 LEU B 41 HIS B 44 5 4 HELIX 15 AB6 ASN B 45 GLY B 63 1 19 HELIX 16 AB7 GLN B 77 GLY B 102 1 26 HELIX 17 AB8 LYS B 103 ALA B 106 5 4 HELIX 18 AB9 HIS B 107 LEU B 117 1 11 HELIX 19 AC1 LEU B 118 PHE B 120 5 3 HELIX 20 AC2 PHE B 128 GLN B 136 5 9 HELIX 21 AC3 ARG B 137 GLN B 152 1 16 CRYST1 52.079 68.629 76.453 90.00 90.00 90.00 P 2 21 21 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 0.019202 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014571 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013080 0.00000 MASTER 271 0 0 21 0 0 0 6 2332 2 0 24 END