PDB Short entry for 6DCE HEADER STRUCTURAL PROTEIN 05-MAY-18 6DCE TITLE X-RAY STRUCTURE OF FIP200 CLAW DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RB1-INDUCIBLE COILED-COIL PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FAK FAMILY KINASE-INTERACTING PROTEIN OF 200 KDA,FIP200; 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: RB1CC1, KIAA0203, RBICC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS AUTOPHAGY, FIP200, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.-Y.SU,J.H.HURLEY REVDAT 3 01-MAY-19 6DCE 1 JRNL REVDAT 2 27-MAR-19 6DCE 1 JRNL REVDAT 1 06-MAR-19 6DCE 0 JRNL AUTH E.TURCO,M.WITT,C.ABERT,T.BOCK-BIERBAUM,M.Y.SU,R.TRAPANNONE, JRNL AUTH 2 M.SZTACHO,A.DANIELI,X.SHI,G.ZAFFAGNINI,A.GAMPER, JRNL AUTH 3 M.SCHUSCHNIG,D.FRACCHIOLLA,D.BERNKLAU,J.ROMANOV,M.HARTL, JRNL AUTH 4 J.H.HURLEY,O.DAUMKE,S.MARTENS JRNL TITL FIP200 CLAW DOMAIN BINDING TO P62 PROMOTES AUTOPHAGOSOME JRNL TITL 2 FORMATION AT UBIQUITIN CONDENSATES. JRNL REF MOL. CELL V. 74 330 2019 JRNL REFN ISSN 1097-4164 JRNL PMID 30853400 JRNL DOI 10.1016/J.MOLCEL.2019.01.035 REMARK 2 REMARK 2 RESOLUTION. 1.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 15835 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.520 REMARK 3 FREE R VALUE TEST SET COUNT : 1508 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 19.6737 - 3.4637 1.00 1424 150 0.1904 0.2343 REMARK 3 2 3.4637 - 2.7516 1.00 1352 142 0.2210 0.2459 REMARK 3 3 2.7516 - 2.4045 1.00 1338 142 0.2388 0.2782 REMARK 3 4 2.4045 - 2.1850 1.00 1320 138 0.2097 0.2487 REMARK 3 5 2.1850 - 2.0285 0.99 1316 139 0.2020 0.2175 REMARK 3 6 2.0285 - 1.9090 0.99 1304 137 0.1952 0.2251 REMARK 3 7 1.9090 - 1.8135 0.97 1267 133 0.1975 0.2328 REMARK 3 8 1.8135 - 1.7346 0.98 1285 135 0.1952 0.1960 REMARK 3 9 1.7346 - 1.6679 0.96 1264 133 0.2157 0.2393 REMARK 3 10 1.6679 - 1.6103 0.95 1235 130 0.2306 0.2668 REMARK 3 11 1.6103 - 1.5600 0.93 1222 129 0.2554 0.2658 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.940 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 : 0.006 789 REMARK 3 ANGLE : 0.819 1065 REMARK 3 CHIRALITY : 0.053 115 REMARK 3 PLANARITY : 0.006 130 REMARK 3 DIHEDRAL : 18.090 468 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 6DCE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000234239. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-18 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 : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16114 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 REMARK 200 RESOLUTION RANGE LOW (A) : 44.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.4, 2 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 40.04900 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 40.04900 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 15.38950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.61000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 15.38950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.61000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.04900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 15.38950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.61000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 40.04900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 15.38950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.61000 REMARK 290 SMTRY3 8 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 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 GLU A 1544 REMARK 465 GLY A 1545 REMARK 465 ALA A 1546 REMARK 465 SER A 1547 REMARK 465 GLY A 1548 REMARK 465 ALA A 1549 REMARK 465 LYS A 1592 REMARK 465 LYS A 1593 REMARK 465 VAL A 1594 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 HOH A 1702 O HOH A 1709 2.01 REMARK 500 O HOH A 1755 O HOH A 1758 2.16 REMARK 500 O HOH A 1701 O HOH A 1754 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 1703 O HOH A 1758 3655 2.18 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 ASP A1516 56.90 30.03 REMARK 500 MSE A1560 -117.80 -123.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1603 DBREF 6DCE A 1494 1594 UNP Q8TDY2 RBCC1_HUMAN 1494 1594 SEQRES 1 A 101 GLU LYS ILE ALA ILE ARG ASP PHE GLN VAL GLY ASP LEU SEQRES 2 A 101 VAL LEU ILE ILE LEU ASP GLU ARG HIS ASP ASN TYR VAL SEQRES 3 A 101 LEU PHE THR VAL SER PRO THR LEU TYR PHE LEU HIS SER SEQRES 4 A 101 GLU SER LEU PRO ALA LEU ASP LEU LYS PRO GLY GLU GLY SEQRES 5 A 101 ALA SER GLY ALA SER ARG ARG PRO TRP VAL LEU GLY LYS SEQRES 6 A 101 VAL MSE GLU LYS GLU TYR CYS GLN ALA LYS LYS ALA GLN SEQRES 7 A 101 ASN ARG PHE LYS VAL PRO LEU GLY THR LYS PHE TYR ARG SEQRES 8 A 101 VAL LYS ALA VAL SER TRP ASN LYS LYS VAL MODRES 6DCE MSE A 1560 MET MODIFIED RESIDUE HET MSE A1560 8 HET SO4 A1601 5 HET SO4 A1602 5 HET SO4 A1603 5 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *70(H2 O) HELIX 1 AA1 SER A 1532 ASP A 1539 5 8 SHEET 1 AA1 6 LEU A1506 ASP A1512 0 SHEET 2 AA1 6 ASN A1517 LEU A1520 -1 O VAL A1519 N ILE A1510 SHEET 3 AA1 6 TYR A1528 LEU A1530 -1 O TYR A1528 N LEU A1520 SHEET 4 AA1 6 LYS A1581 SER A1589 1 O VAL A1585 N PHE A1529 SHEET 5 AA1 6 TRP A1554 GLN A1566 -1 N CYS A1565 O PHE A1582 SHEET 6 AA1 6 LEU A1506 ASP A1512 -1 N ILE A1509 O VAL A1555 LINK C VAL A1559 N MSE A1560 1555 1555 1.32 LINK C MSE A1560 N GLU A1561 1555 1555 1.34 LINK NH1 ARG A1584 O3 SO4 A1601 1555 1555 1.30 SITE 1 AC1 4 HIS A1531 SER A1532 ARG A1573 ARG A1584 SITE 1 AC2 2 ARG A1573 ARG A1584 SITE 1 AC3 2 ASN A1572 ARG A1573 CRYST1 30.779 89.220 80.098 90.00 90.00 90.00 C 2 2 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 0.032490 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011208 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012485 0.00000