HEADER MOTOR PROTEIN 31-MAR-19 6OFP TITLE STRUCTURE OF THE C-TERMINAL CARGO BINDING DOMAIN OF HUMAN BICAUDAL D2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN BICAUDAL D HOMOLOG 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BIC-D 2; 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: BICD2, KIAA0699; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID PET28A KEYWDS BICAUDAL D2, DYNEIN, DYNEIN ADAPTOR, COILED-COIL, REGISTRY SHIFT, KEYWDS 2 SPINAL MUSCULAR ATROPHY, CYTOSKELETAL MOTOR, MOTOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.R.NOELL,E.W.DEBLER,H.CUI,S.R.SOLMAZ REVDAT 5 11-OCT-23 6OFP 1 REMARK REVDAT 4 27-NOV-19 6OFP 1 REMARK REVDAT 3 14-AUG-19 6OFP 1 JRNL REVDAT 2 07-AUG-19 6OFP 1 JRNL REVDAT 1 24-JUL-19 6OFP 0 JRNL AUTH C.R.NOELL,J.Y.LOH,E.W.DEBLER,K.M.LOFTUS,H.CUI,B.B.RUSS, JRNL AUTH 2 K.ZHANG,P.GOYAL,S.R.SOLMAZ JRNL TITL ROLE OF COILED-COIL REGISTRY SHIFTS IN THE ACTIVATION OF JRNL TITL 2 HUMAN BICAUDAL D2 FOR DYNEIN RECRUITMENT UPON CARGO BINDING. JRNL REF J PHYS CHEM LETT V. 10 4362 2019 JRNL REFN ESSN 1948-7185 JRNL PMID 31306018 JRNL DOI 10.1021/ACS.JPCLETT.9B01865 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1819 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 13113 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1313 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 37.5576 - 4.1699 0.98 1408 155 0.2419 0.2532 REMARK 3 2 4.1699 - 3.3104 1.00 1404 156 0.1927 0.2188 REMARK 3 3 3.3104 - 2.8921 0.99 1365 153 0.2270 0.2327 REMARK 3 4 2.8921 - 2.6278 0.99 1361 150 0.2226 0.2948 REMARK 3 5 2.6278 - 2.4395 0.98 1333 149 0.2259 0.2842 REMARK 3 6 2.4395 - 2.2957 0.97 1326 147 0.2245 0.2498 REMARK 3 7 2.2957 - 2.1807 0.95 1306 149 0.2275 0.2815 REMARK 3 8 2.1807 - 2.0858 0.90 1236 137 0.2624 0.3326 REMARK 3 9 2.0858 - 2.0055 0.78 1061 117 0.2935 0.3679 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.00 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 : 0.003 1478 REMARK 3 ANGLE : 0.667 1973 REMARK 3 CHIRALITY : 0.027 231 REMARK 3 PLANARITY : 0.003 252 REMARK 3 DIHEDRAL : 14.835 589 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 35.9796 -6.1347 55.2714 REMARK 3 T TENSOR REMARK 3 T11: 0.2820 T22: 0.2835 REMARK 3 T33: 0.2909 T12: 0.0043 REMARK 3 T13: -0.0155 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 0.0084 L22: 0.0218 REMARK 3 L33: 0.0910 L12: 0.0170 REMARK 3 L13: 0.0248 L23: 0.0251 REMARK 3 S TENSOR REMARK 3 S11: 0.0392 S12: 0.1321 S13: -0.0496 REMARK 3 S21: -0.0029 S22: -0.0135 S23: -0.0089 REMARK 3 S31: 0.0043 S32: 0.0801 S33: -0.0000 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 6OFP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-APR-19. REMARK 100 THE DEPOSITION ID IS D_1000240584. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.05 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 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 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13628 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.34000 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX DEV_1819 REMARK 200 STARTING MODEL: 4YTD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, PH 8.05, 26% TERT-BUTANOL, REMARK 280 40 MM CACL2, 60 MM 1,6-HEXANEDIOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 36.84700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.47900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 36.84700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.47900 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: 4330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 111 LIES ON A SPECIAL POSITION. 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 ASP A 92 REMARK 465 HIS A 93 REMARK 465 GLU A 94 REMARK 465 HIS B 93 REMARK 465 GLU B 94 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 129 DISTANCE = 6.78 ANGSTROMS REMARK 525 HOH A 130 DISTANCE = 7.45 ANGSTROMS REMARK 525 HOH B 122 DISTANCE = 6.00 ANGSTROMS DBREF 6OFP A 5 94 UNP Q8TD16 BICD2_HUMAN 715 804 DBREF 6OFP B 5 94 UNP Q8TD16 BICD2_HUMAN 715 804 SEQADV 6OFP GLY A 1 UNP Q8TD16 EXPRESSION TAG SEQADV 6OFP SER A 2 UNP Q8TD16 EXPRESSION TAG SEQADV 6OFP HIS A 3 UNP Q8TD16 EXPRESSION TAG SEQADV 6OFP MET A 4 UNP Q8TD16 EXPRESSION TAG SEQADV 6OFP GLY B 1 UNP Q8TD16 EXPRESSION TAG SEQADV 6OFP SER B 2 UNP Q8TD16 EXPRESSION TAG SEQADV 6OFP HIS B 3 UNP Q8TD16 EXPRESSION TAG SEQADV 6OFP MET B 4 UNP Q8TD16 EXPRESSION TAG SEQRES 1 A 94 GLY SER HIS MET TYR GLU ASN GLU LYS ALA MET VAL THR SEQRES 2 A 94 GLU THR MET MET LYS LEU ARG ASN GLU LEU LYS ALA LEU SEQRES 3 A 94 LYS GLU ASP ALA ALA THR PHE SER SER LEU ARG ALA MET SEQRES 4 A 94 PHE ALA THR ARG CYS ASP GLU TYR ILE THR GLN LEU ASP SEQRES 5 A 94 GLU MET GLN ARG GLN LEU ALA ALA ALA GLU ASP GLU LYS SEQRES 6 A 94 LYS THR LEU ASN SER LEU LEU ARG MET ALA ILE GLN GLN SEQRES 7 A 94 LYS LEU ALA LEU THR GLN ARG LEU GLU LEU LEU GLU LEU SEQRES 8 A 94 ASP HIS GLU SEQRES 1 B 94 GLY SER HIS MET TYR GLU ASN GLU LYS ALA MET VAL THR SEQRES 2 B 94 GLU THR MET MET LYS LEU ARG ASN GLU LEU LYS ALA LEU SEQRES 3 B 94 LYS GLU ASP ALA ALA THR PHE SER SER LEU ARG ALA MET SEQRES 4 B 94 PHE ALA THR ARG CYS ASP GLU TYR ILE THR GLN LEU ASP SEQRES 5 B 94 GLU MET GLN ARG GLN LEU ALA ALA ALA GLU ASP GLU LYS SEQRES 6 B 94 LYS THR LEU ASN SER LEU LEU ARG MET ALA ILE GLN GLN SEQRES 7 B 94 LYS LEU ALA LEU THR GLN ARG LEU GLU LEU LEU GLU LEU SEQRES 8 B 94 ASP HIS GLU FORMUL 3 HOH *52(H2 O) HELIX 1 AA1 GLY A 1 ALA A 31 1 31 HELIX 2 AA2 THR A 32 GLU A 90 1 59 HELIX 3 AA3 SER B 2 LEU B 91 1 90 CRYST1 73.694 36.958 78.706 90.00 107.41 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 0.013570 0.000000 0.004254 0.00000 SCALE2 0.000000 0.027058 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013315 0.00000