HEADER TRANSPORT PROTEIN 18-JUN-14 4TS6 TITLE CRYSTAL STRUCTURE OF THE RIM C2A DOMAIN FROM DROSOPHILA. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAB3 INTERACTING MOLECULE VARIANT 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 836-962; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: RIM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS C2A DOMAIN, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.N.HATZOPOULOS,J.SHIROMA,I.VAKONAKIS REVDAT 2 20-DEC-23 4TS6 1 REMARK REVDAT 1 01-JUL-15 4TS6 0 JRNL AUTH M.PAUL,M.HECKMANN,J.GEHRING,R.J.KITTEL,S.ULZHOEFER,K.NEUSER, JRNL AUTH 2 A.DIANTONIO,G.N.HATZOPOULOS,J.SHIROMA,I.VAKONAKIS, JRNL AUTH 3 T.LANGENHAN JRNL TITL CRYSTAL STRUCTURE OF THE RIM C2A DOMAIN FROM DROSOPHILA. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13140 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 648 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 0.0000 - 3.2832 1.00 2629 139 0.1704 0.1880 REMARK 3 2 3.2832 - 2.6059 1.00 2517 120 0.1909 0.2550 REMARK 3 3 2.6059 - 2.2765 1.00 2442 132 0.1954 0.2093 REMARK 3 4 2.2765 - 2.0683 1.00 2486 120 0.1962 0.2471 REMARK 3 5 2.0683 - 1.9201 1.00 2418 137 0.2267 0.2950 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.69 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 : 0.007 1058 REMARK 3 ANGLE : 1.190 1436 REMARK 3 CHIRALITY : 0.086 159 REMARK 3 PLANARITY : 0.004 184 REMARK 3 DIHEDRAL : 13.690 392 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -1 THROUGH 962) REMARK 3 ORIGIN FOR THE GROUP (A): 14.3144 4.2403 -17.8546 REMARK 3 T TENSOR REMARK 3 T11: 0.1424 T22: 0.2094 REMARK 3 T33: 0.2187 T12: -0.0329 REMARK 3 T13: 0.0283 T23: -0.0483 REMARK 3 L TENSOR REMARK 3 L11: 2.5579 L22: 2.9456 REMARK 3 L33: 3.2253 L12: -0.7521 REMARK 3 L13: -0.7027 L23: 1.0375 REMARK 3 S TENSOR REMARK 3 S11: -0.0471 S12: -0.3888 S13: 0.2443 REMARK 3 S21: -0.0716 S22: 0.1760 S23: -0.3199 REMARK 3 S31: -0.0017 S32: 0.1437 S33: -0.1061 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 4TS6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000202188. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999 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, XSCALE REMARK 200 DATA SCALING SOFTWARE : AIMLESS 3.11, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13188 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 65.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.64300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.970 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MRBUMP REMARK 200 STARTING MODEL: 2BWQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M TRI-LITHIUM CITRATE, 20% W/V PEG REMARK 280 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 16.04000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.68500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.68500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.04000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.35000 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: 220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6870 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 -7 REMARK 465 PRO A -6 REMARK 465 LEU A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 ILE A -2 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 O SER A 870 O HOH A 1101 2.10 REMARK 500 OG1 THR A 863 OE1 GLU A 902 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 THR A 899 76.28 38.34 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 A1193 DISTANCE = 5.85 ANGSTROMS 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 1001 DBREF 4TS6 A -2 962 UNP V5M2P5 V5M2P5_DROME 836 962 SEQADV 4TS6 GLY A -7 UNP V5M2P5 EXPRESSION TAG SEQADV 4TS6 PRO A -6 UNP V5M2P5 EXPRESSION TAG SEQADV 4TS6 LEU A -5 UNP V5M2P5 EXPRESSION TAG SEQADV 4TS6 GLY A -4 UNP V5M2P5 EXPRESSION TAG SEQADV 4TS6 SER A -3 UNP V5M2P5 EXPRESSION TAG SEQRES 1 A 132 GLY PRO LEU GLY SER ILE PRO ILE GLU GLY ARG LEU GLN SEQRES 2 A 132 LEU LYS LEU GLY TYR ASP GLN ASN THR LEU GLN LEU ILE SEQRES 3 A 132 VAL THR LEU VAL CYS ALA THR GLY LEU SER LEU ARG GLN SEQRES 4 A 132 SER GLY ALA GLY ARG ASN PRO TYR ALA LYS VAL PHE LEU SEQRES 5 A 132 LEU PRO ASP ARG SER HIS LYS SER LYS ARG ARG THR LYS SEQRES 6 A 132 THR VAL GLY THR THR CYS GLU PRO ARG TRP GLY GLN THR SEQRES 7 A 132 PHE VAL TYR SER GLY LEU ARG ARG CYS ASP LEU ASN GLY SEQRES 8 A 132 ARG LEU LEU GLU VAL THR LEU TRP ASP TYR VAL ARG TYR SEQRES 9 A 132 GLY ALA ASN ASP PHE ILE GLY GLU VAL VAL ILE ASP LEU SEQRES 10 A 132 ALA HIS HIS ILE LEU ASP ASP GLU ALA GLU TRP TYR GLN SEQRES 11 A 132 LEU GLN HET GOL A1001 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *94(H2 O) HELIX 1 AA1 ARG A 915 ASN A 920 5 6 HELIX 2 AA2 ALA A 948 HIS A 950 5 3 SHEET 1 AA1 4 ARG A 904 TYR A 911 0 SHEET 2 AA1 4 GLN A 854 THR A 863 -1 N VAL A 857 O PHE A 909 SHEET 3 AA1 4 ARG A 841 ASP A 849 -1 N GLY A 847 O ILE A 856 SHEET 4 AA1 4 ASP A 953 GLN A 960 -1 O ASP A 954 N LEU A 846 SHEET 1 AA2 4 ARG A 892 ARG A 893 0 SHEET 2 AA2 4 PRO A 876 LEU A 883 -1 N VAL A 880 O ARG A 892 SHEET 3 AA2 4 LEU A 923 ASP A 930 -1 O THR A 927 N LYS A 879 SHEET 4 AA2 4 ASP A 938 ASP A 946 -1 O GLY A 941 N LEU A 928 CISPEP 1 LEU A 883 PRO A 884 0 9.17 SITE 1 AC1 5 TRP A 929 ALA A 936 ASN A 937 HOH A1102 SITE 2 AC1 5 HOH A1111 CRYST1 32.080 38.700 131.370 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 0.031172 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025840 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007612 0.00000