HEADER LIGASE 10-SEP-25 9SNF TITLE CTLH-CRA DOMAIN OF MURINE RANBP10 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 9SNF 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. 2.07 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 72.3 REMARK 3 NUMBER OF REFLECTIONS : 14583 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 699 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 38.5300 - 3.5400 0.99 3999 196 0.1747 0.2106 REMARK 3 2 3.5400 - 2.8100 0.99 3793 212 0.2108 0.2682 REMARK 3 3 2.8100 - 2.4500 0.98 3758 173 0.2465 0.2956 REMARK 3 4 2.4500 - 2.2300 0.51 1920 101 0.2765 0.3479 REMARK 3 5 2.2300 - 2.0700 0.11 414 17 0.3177 0.2751 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) : 0.246 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.854 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.76 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 : 0.002 2207 REMARK 3 ANGLE : 0.369 2978 REMARK 3 CHIRALITY : 0.031 330 REMARK 3 PLANARITY : 0.004 397 REMARK 3 DIHEDRAL : 12.543 844 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 9SNF 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_1292150693. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9677 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14606 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.069 REMARK 200 RESOLUTION RANGE LOW (A) : 44.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.16600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 57.4 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : 1.79700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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 (%): 49.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 7.8, 15% PEG 3350, VAPOR REMARK 280 DIFFUSION, HANGING 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 37.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.19300 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.75000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.19300 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 -1 REMARK 465 PRO A 0 REMARK 465 SER A 64 REMARK 465 LEU A 65 REMARK 465 SER A 66 REMARK 465 SER A 67 REMARK 465 GLY A 68 REMARK 465 GLY A 69 REMARK 465 ASN A 70 REMARK 465 GLN A 71 REMARK 465 GLY B -1 REMARK 465 PRO B 0 REMARK 465 GLU B 1 REMARK 465 SER B 60 REMARK 465 GLU B 61 REMARK 465 VAL B 62 REMARK 465 ARG B 63 REMARK 465 SER B 64 REMARK 465 LEU B 65 REMARK 465 SER B 66 REMARK 465 SER B 67 REMARK 465 GLY B 68 DBREF 9SNF A 1 67 UNP Q6VN19 RBP10_MOUSE 287 353 DBREF 9SNF A 68 146 UNP Q6VN19 RBP10_MOUSE 502 580 DBREF 9SNF B 1 67 UNP Q6VN19 RBP10_MOUSE 287 353 DBREF 9SNF B 68 146 UNP Q6VN19 RBP10_MOUSE 502 580 SEQADV 9SNF GLY A -1 UNP Q6VN19 EXPRESSION TAG SEQADV 9SNF PRO A 0 UNP Q6VN19 EXPRESSION TAG SEQADV 9SNF GLY B -1 UNP Q6VN19 EXPRESSION TAG SEQADV 9SNF PRO B 0 UNP Q6VN19 EXPRESSION TAG 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 GLN 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 PHE SER LEU LEU ALA TYR SER SEQRES 10 A 148 ASP PRO TRP SER CYS PRO VAL 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 GLN 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 PHE SER LEU LEU ALA TYR SER SEQRES 10 B 148 ASP PRO TRP SER CYS PRO VAL 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 *63(H2 O) HELIX 1 AA1 GLU A 2 GLU A 18 1 17 HELIX 2 AA2 ARG A 20 TYR A 32 1 13 HELIX 3 AA3 LEU A 35 HIS A 38 5 4 HELIX 4 AA4 ASN A 39 ASN A 56 1 18 HELIX 5 AA5 ALA A 73 GLY A 96 1 24 HELIX 6 AA6 ASN A 98 LEU A 111 1 14 HELIX 7 AA7 LEU A 112 TYR A 114 5 3 HELIX 8 AA8 ASP A 116 CYS A 120 5 5 HELIX 9 AA9 VAL A 122 GLN A 130 5 9 HELIX 10 AB1 ARG A 131 GLN A 146 1 16 HELIX 11 AB2 GLN B 3 GLU B 18 1 16 HELIX 12 AB3 ARG B 20 TYR B 32 1 13 HELIX 13 AB4 LEU B 35 HIS B 38 5 4 HELIX 14 AB5 ASN B 39 GLY B 57 1 19 HELIX 15 AB6 ASN B 70 GLY B 96 1 27 HELIX 16 AB7 ASN B 98 LEU B 111 1 14 HELIX 17 AB8 LEU B 112 TYR B 114 5 3 HELIX 18 AB9 ASP B 116 CYS B 120 5 5 HELIX 19 AC1 VAL B 122 GLN B 130 5 9 HELIX 20 AC2 ARG B 131 GLN B 146 1 16 CRYST1 55.331 75.500 76.386 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 0.018073 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013245 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013091 0.00000 MASTER 227 0 0 20 0 0 0 6 2236 2 0 24 END