HEADER PROTEIN TRANSPORT 28-JUL-12 3VVV TITLE SKICH DOMAIN OF NDP52 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALCIUM-BINDING AND COILED-COIL DOMAIN-CONTAINING PROTEIN COMPND 3 2; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 21-141; COMPND 6 SYNONYM: ANTIGEN NUCLEAR DOT 52 KDA PROTEIN, NUCLEAR DOMAIN 10 COMPND 7 PROTEIN NDP52, NUCLEAR DOMAIN 10 PROTEIN 52, NUCLEAR DOT PROTEIN 52; COMPND 8 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: CALCOCO2, NDP52; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AUTOPHAGY ADAPTOR PROTEIN, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.AKUTSU,N.V.MUHLINEN,F.RANDOW,D.KOMANDER REVDAT 2 20-MAR-24 3VVV 1 SEQADV REVDAT 1 27-FEB-13 3VVV 0 JRNL AUTH N.V.MUHLINEN,M.AKUTSU,B.J.RAVENHILL,A.FOEGLEIN,S.BLOOR, JRNL AUTH 2 T.J.RUTHERFORD,S.M.FREUND,D.KOMANDER,F.RANDOW JRNL TITL LC3C, BOUND SELECTIVELY BY A NONCANONICAL LIR MOTIF IN JRNL TITL 2 NDP52, IS REQUIRED FOR ANTIBACTERIAL AUTOPHAGY JRNL REF MOL.CELL V. 48 329 2012 JRNL REFN ISSN 1097-2765 JRNL PMID 23022382 JRNL DOI 10.1016/J.MOLCEL.2012.08.024 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_723 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 27807 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1361 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 23.2693 - 2.9068 0.95 2730 127 0.1709 0.2012 REMARK 3 2 2.9068 - 2.3079 0.97 2654 121 0.1612 0.1793 REMARK 3 3 2.3079 - 2.0163 0.99 2658 135 0.1446 0.1882 REMARK 3 4 2.0163 - 1.8321 1.00 2610 186 0.1293 0.1639 REMARK 3 5 1.8321 - 1.7008 1.00 2644 143 0.1160 0.1583 REMARK 3 6 1.7008 - 1.6005 1.00 2637 140 0.1266 0.1741 REMARK 3 7 1.6005 - 1.5204 1.00 2637 128 0.1380 0.1952 REMARK 3 8 1.5204 - 1.4542 1.00 2614 132 0.1686 0.2220 REMARK 3 9 1.4542 - 1.3983 1.00 2617 134 0.1859 0.2579 REMARK 3 10 1.3983 - 1.3500 1.00 2645 115 0.1992 0.2328 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 36.87 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.41700 REMARK 3 B22 (A**2) : -0.29100 REMARK 3 B33 (A**2) : 2.70800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.010 977 REMARK 3 ANGLE : 1.272 1334 REMARK 3 CHIRALITY : 0.106 131 REMARK 3 PLANARITY : 0.008 175 REMARK 3 DIHEDRAL : 13.147 350 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 3VVV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000095564. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9395 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27862 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 26.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.55900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG4000, 0.1M TRIS , PH 8.5, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 293K 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 18.30500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.20000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.73000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.20000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.30500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.73000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC 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 BIOMT1 2 -1.000000 0.000000 0.000000 -36.61000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -18.73000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -45.20000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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 LEU A 81 REMARK 465 ASN A 82 REMARK 465 ASN A 83 REMARK 465 LYS A 84 REMARK 465 SER A 85 REMARK 465 ALA A 86 REMARK 465 ILE A 133 REMARK 465 LEU A 134 REMARK 465 VAL A 135 REMARK 465 VAL A 136 REMARK 465 THR A 137 REMARK 465 THR A 138 REMARK 465 GLN A 139 REMARK 465 GLY A 140 REMARK 465 GLU A 141 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 GLU A 128 CG CD OE1 OE2 REMARK 470 GLU A 130 CG CD OE1 OE2 REMARK 470 GLU A 131 CG CD OE1 OE2 REMARK 470 ASP A 132 CG OD1 OD2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VVW RELATED DB: PDB DBREF 3VVV A 21 141 UNP Q13137 CACO2_HUMAN 21 141 SEQADV 3VVV GLY A 19 UNP Q13137 EXPRESSION TAG SEQADV 3VVV PRO A 20 UNP Q13137 EXPRESSION TAG SEQRES 1 A 123 GLY PRO SER GLN VAL ILE PHE ASN SER VAL GLU LYS PHE SEQRES 2 A 123 TYR ILE PRO GLY GLY ASP VAL THR CYS HIS TYR THR PHE SEQRES 3 A 123 THR GLN HIS PHE ILE PRO ARG ARG LYS ASP TRP ILE GLY SEQRES 4 A 123 ILE PHE ARG VAL GLY TRP LYS THR THR ARG GLU TYR TYR SEQRES 5 A 123 THR PHE MET TRP VAL THR LEU PRO ILE ASP LEU ASN ASN SEQRES 6 A 123 LYS SER ALA LYS GLN GLN GLU VAL GLN PHE LYS ALA TYR SEQRES 7 A 123 TYR LEU PRO LYS ASP ASP GLU TYR TYR GLN PHE CYS TYR SEQRES 8 A 123 VAL ASP GLU ASP GLY VAL VAL ARG GLY ALA SER ILE PRO SEQRES 9 A 123 PHE GLN PHE ARG PRO GLU ASN GLU GLU ASP ILE LEU VAL SEQRES 10 A 123 VAL THR THR GLN GLY GLU FORMUL 2 HOH *178(H2 O) HELIX 1 1 THR A 65 TYR A 69 5 5 HELIX 2 2 LYS A 94 LEU A 98 5 5 SHEET 1 A 3 VAL A 23 ASN A 26 0 SHEET 2 A 3 VAL A 38 PHE A 44 -1 O THR A 43 N ILE A 24 SHEET 3 A 3 GLN A 89 PHE A 93 -1 O VAL A 91 N CYS A 40 SHEET 1 B 2 PHE A 31 TYR A 32 0 SHEET 2 B 2 GLN A 124 PHE A 125 1 O GLN A 124 N TYR A 32 SHEET 1 C 4 THR A 71 TRP A 74 0 SHEET 2 C 4 TRP A 55 ARG A 60 -1 N ILE A 56 O MET A 73 SHEET 3 C 4 TYR A 105 VAL A 110 -1 O VAL A 110 N TRP A 55 SHEET 4 C 4 VAL A 116 ALA A 119 -1 O ARG A 117 N TYR A 109 CISPEP 1 LEU A 77 PRO A 78 0 -7.25 CRYST1 36.610 37.460 90.400 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 0.027315 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026695 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011062 0.00000