HEADER RIM-BINDING PROTEIN 08-APR-15 4Z8A TITLE SH3-III OF DROSOPHILA RIM-BINDING PROTEIN BOUND TO A CACOPHONY DERIVED TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIM-BINDING PROTEIN, ISOFORM F; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1443-1507; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: VOLTAGE-DEPENDENT CALCIUM CHANNEL TYPE A SUBUNIT ALPHA-1; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 1688-1702; COMPND 10 SYNONYM: PROTEIN CACOPHONY,PROTEIN NIGHTBLIND A,PROTEIN NO-ON- COMPND 11 TRANSIENT B,DMCA1A; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: N-TERMINUS IS ACETYLATED, C-TERMINUS IS AMIDATED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: RBP, DMEL_CG43073; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX6P1; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 13 ORGANISM_COMMON: FRUIT FLY; SOURCE 14 ORGANISM_TAXID: 7227 KEYWDS SYNAPSE, ACTIVE ZONE, SH3 DOMAIN, RIM-BINDING PROTEIN, CACOPHONY KEYWDS 2 PEPTIDE EXPDTA X-RAY DIFFRACTION AUTHOR J.H.DRILLER,N.HOLTON,M.SIEBERT,A.M.BOEHME,M.C.WAHL,S.J.SIGRIST,B.LOLL REVDAT 3 10-JAN-24 4Z8A 1 REMARK REVDAT 2 26-AUG-15 4Z8A 1 JRNL REVDAT 1 05-AUG-15 4Z8A 0 JRNL AUTH M.SIEBERT,M.A.BOHME,J.H.DRILLER,H.BABIKIR,M.M.MAMPELL,U.REY, JRNL AUTH 2 N.RAMESH,T.MATKOVIC,N.HOLTON,S.REDDY-ALLA,F.GOTTFERT, JRNL AUTH 3 D.KAMIN,C.QUENTIN,S.KLINEDINST,T.F.ANDLAUER,S.W.HELL, JRNL AUTH 4 C.A.COLLINS,M.C.WAHL,B.LOLL,S.J.SIGRIST JRNL TITL A HIGH AFFINITY RIM-BINDING PROTEIN/APLIP1 INTERACTION JRNL TITL 2 PREVENTS THE FORMATION OF ECTOPIC AXONAL ACTIVE ZONES. JRNL REF ELIFE V. 4 2015 JRNL REFN ESSN 2050-084X JRNL PMID 26274777 JRNL DOI 10.7554/ELIFE.06935 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 10452 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 523 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 43.6766 - 2.7923 0.98 2583 136 0.1411 0.1768 REMARK 3 2 2.7923 - 2.2164 0.99 2510 133 0.1618 0.2339 REMARK 3 3 2.2164 - 1.9362 0.99 2481 130 0.1650 0.2265 REMARK 3 4 1.9362 - 1.7592 0.94 2355 124 0.2162 0.2573 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.010 762 REMARK 3 ANGLE : 1.205 1044 REMARK 3 CHIRALITY : 0.051 112 REMARK 3 PLANARITY : 0.007 143 REMARK 3 DIHEDRAL : 11.572 304 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 4Z8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208628. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10690 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.55700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 4Z88 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES PH 6.5, 200MM REMARK 280 LITHIUMSULFAT, 30% (V/V) PEG 400, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 26.06500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.12300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 36.79100 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.06500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.12300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 36.79100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.06500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.12300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 36.79100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.06500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 27.12300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 36.79100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 A1654 LIES ON A SPECIAL POSITION. REMARK 375 HOH B1832 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1651 O HOH B 1822 7545 2.16 REMARK 500 O HOH A 1668 O HOH A 1670 8555 2.18 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 A1678 DISTANCE = 6.70 ANGSTROMS DBREF1 4Z8A A 1443 1507 UNP A0A0B4JDC9_DROME DBREF2 4Z8A A A0A0B4JDC9 1443 1507 DBREF 4Z8A B 1685 1699 UNP P91645 CAC1A_DROME 1688 1702 SEQADV 4Z8A GLY A 1433 UNP A0A0B4JDC EXPRESSION TAG SEQADV 4Z8A PRO A 1434 UNP A0A0B4JDC EXPRESSION TAG SEQADV 4Z8A LEU A 1435 UNP A0A0B4JDC EXPRESSION TAG SEQADV 4Z8A GLY A 1436 UNP A0A0B4JDC EXPRESSION TAG SEQADV 4Z8A SER A 1437 UNP A0A0B4JDC EXPRESSION TAG SEQADV 4Z8A PRO A 1438 UNP A0A0B4JDC EXPRESSION TAG SEQADV 4Z8A GLU A 1439 UNP A0A0B4JDC EXPRESSION TAG SEQADV 4Z8A PHE A 1440 UNP A0A0B4JDC EXPRESSION TAG SEQADV 4Z8A ASN A 1441 UNP A0A0B4JDC EXPRESSION TAG SEQADV 4Z8A ARG A 1442 UNP A0A0B4JDC EXPRESSION TAG SEQADV 4Z8A ACE B 1684 UNP P91645 ACETYLATION SEQADV 4Z8A NH2 B 1700 UNP P91645 AMIDATION SEQRES 1 A 75 GLY PRO LEU GLY SER PRO GLU PHE ASN ARG PRO VAL LYS SEQRES 2 A 75 ARG MET ILE ALA LEU TYR ASP TYR ASP PRO GLN GLU LEU SEQRES 3 A 75 SER PRO ASN VAL ASP ALA GLU GLN VAL GLU LEU CYS PHE SEQRES 4 A 75 LYS THR GLY GLU ILE ILE LEU VAL TYR GLY ASP MET ASP SEQRES 5 A 75 GLU ASP GLY PHE TYR MET GLY GLU LEU ASP GLY VAL ARG SEQRES 6 A 75 GLY LEU VAL PRO SER ASN PHE LEU ALA ASP SEQRES 1 B 17 ACE ILE GLY ARG ARG LEU PRO PRO THR PRO SER LYS PRO SEQRES 2 B 17 SER THR LEU NH2 HET ACE B1684 3 HET NH2 B1700 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 2 ACE C2 H4 O FORMUL 2 NH2 H2 N FORMUL 3 HOH *110(H2 O) HELIX 1 AA1 ASP A 1454 SER A 1459 1 6 HELIX 2 AA2 ASP A 1463 GLU A 1468 1 6 HELIX 3 AA3 ASN A 1503 LEU A 1505 5 3 SHEET 1 AA1 4 VAL A1444 ILE A1448 0 SHEET 2 AA1 4 ILE A1476 TYR A1480 -1 O VAL A1479 N LYS A1445 SHEET 3 AA1 4 PHE A1488 LEU A1493 -1 O MET A1490 N TYR A1480 SHEET 4 AA1 4 VAL A1496 PRO A1501 -1 O VAL A1496 N LEU A1493 LINK C ACE B1684 N ILE B1685 1555 1555 1.33 LINK C LEU B1699 N NH2 B1700 1555 1555 1.33 CRYST1 52.130 54.246 73.582 90.00 90.00 90.00 I 2 2 2 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 0.019183 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018435 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013590 0.00000