HEADER PROTEIN BINDING 21-OCT-11 3UAF TITLE CRYSTAL STRUCTURE OF A TTR-52 MUTANT OF C. ELEGANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TTR-52; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 21-135; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA BARREL/SANDWICH, CELL ENGULFMENT, SECRETED, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.Y.KANG,D.F.ZHAO,H.H.LIANG,B.LIU,Q.W.LIU,X.C.WANG,Y.F.LIU REVDAT 1 24-OCT-12 3UAF 0 JRNL AUTH Y.Y.KANG,D.F.ZHAO,H.H.LIANG,B.LIU,Y.ZHANG,Q.W.LIU,X.C.WANG, JRNL AUTH 2 Y.F.LIU JRNL TITL STRUCTURAL STUDY OF TTR-52 REVEALS THE MECHANISM BY WHICH A JRNL TITL 2 BRIDGING MOLECULE MEDIATES APOPTOTIC CELL ENGULFMENT JRNL REF GENES DEV. V. 26 1339 2012 JRNL REFN ISSN 0890-9369 JRNL PMID 22713871 JRNL DOI 10.1101/GAD.187815.112 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 7360 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.690 REMARK 3 FREE R VALUE TEST SET COUNT : 713 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 33.6597 - 3.4363 1.00 1370 166 0.1679 0.1934 REMARK 3 2 3.4363 - 2.7279 1.00 1327 154 0.1788 0.2451 REMARK 3 3 2.7279 - 2.3831 0.99 1339 131 0.1763 0.2365 REMARK 3 4 2.3831 - 2.1653 0.98 1317 119 0.1646 0.2244 REMARK 3 5 2.1653 - 2.0101 0.97 1294 143 0.1814 0.2500 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 : 0.38 REMARK 3 B_SOL : 49.48 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.91060 REMARK 3 B22 (A**2) : -0.84200 REMARK 3 B33 (A**2) : 1.75260 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.23150 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 : 0.007 942 REMARK 3 ANGLE : 1.105 1286 REMARK 3 CHIRALITY : 0.078 142 REMARK 3 PLANARITY : 0.005 170 REMARK 3 DIHEDRAL : 13.065 339 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 3UAF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-OCT-11. REMARK 100 THE RCSB ID CODE IS RCSB068508. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-07; 10-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; N REMARK 200 RADIATION SOURCE : ROTATING ANODE; ROTATING ANODE REMARK 200 BEAMLINE : NULL; NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT; RIGAKU REMARK 200 FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 1.5418 REMARK 200 MONOCHROMATOR : SI200; SI200 REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++; RIGAKU RAXIS REMARK 200 IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7360 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 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) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS 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 (%): 43.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M SOLDIUM REMARK 280 ACETATE, 35% PEGME2000, PH 4.5, EVAPORATION, TEMPERATURE 289K 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 35.16050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.68400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.16050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.68400 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: 1400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 56.05716 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 47.15488 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 A 216 LIES ON A SPECIAL POSITION. 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 ASP A 101 O HOH A 301 1.89 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 A 36 87.78 -161.59 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 A 311 DISTANCE = 5.33 ANGSTROMS REMARK 525 HOH A 313 DISTANCE = 6.42 ANGSTROMS DBREF 3UAF A 21 135 UNP G5ED35 G5ED35_CAEEL 21 135 SEQADV 3UAF ALA A 50 UNP G5ED35 GLU 50 ENGINEERED MUTATION SEQADV 3UAF ALA A 51 UNP G5ED35 ASP 51 ENGINEERED MUTATION SEQADV 3UAF ALA A 52 UNP G5ED35 SER 52 ENGINEERED MUTATION SEQADV 3UAF ALA A 53 UNP G5ED35 LEU 53 ENGINEERED MUTATION SEQADV 3UAF ALA A 54 UNP G5ED35 PRO 54 ENGINEERED MUTATION SEQADV 3UAF ALA A 55 UNP G5ED35 LEU 55 ENGINEERED MUTATION SEQADV 3UAF HIS A 136 UNP G5ED35 EXPRESSION TAG SEQADV 3UAF HIS A 137 UNP G5ED35 EXPRESSION TAG SEQRES 1 A 117 LYS THR SER CYS LEU MET ALA THR GLY VAL LEU LYS CYS SEQRES 2 A 117 PRO THR ASP PRO GLU ALA VAL LYS LYS VAL HIS ILE ASP SEQRES 3 A 117 LEU TRP ASP ALA ALA ALA ALA ALA ALA GLU SER ASP ASP SEQRES 4 A 117 LEU MET GLY ARG THR TRP SER ASP ARG ASN GLY ASN PHE SEQRES 5 A 117 GLN VAL THR GLY CYS ALA SER ASP PHE GLY PRO ILE ASN SEQRES 6 A 117 THR PRO ASP PRO TYR LEU TYR ILE GLN HIS ASN CYS PRO SEQRES 7 A 117 HIS ARG ASP SER ASN ALA THR ASN PRO ILE GLN ILE ASP SEQRES 8 A 117 VAL ILE PRO LEU PHE LEU PRO SER ILE VAL ARG LEU GLY SEQRES 9 A 117 ASN VAL TYR LEU ASP ARG TYR LEU GLU ASP TYR HIS HIS FORMUL 2 HOH *118(H2 O) HELIX 1 1 ASP A 36 LYS A 41 5 6 HELIX 2 2 ALA A 50 ALA A 55 1 6 HELIX 3 3 TYR A 131 HIS A 137 1 7 SHEET 1 A 3 ASN A 71 ALA A 78 0 SHEET 2 A 3 SER A 23 LYS A 32 -1 N LEU A 25 O GLY A 76 SHEET 3 A 3 ILE A 120 TYR A 127 1 O VAL A 121 N MET A 26 SHEET 1 B 4 LEU A 60 TRP A 65 0 SHEET 2 B 4 HIS A 44 ASP A 49 -1 N ILE A 45 O THR A 64 SHEET 3 B 4 PRO A 89 GLN A 94 -1 O TYR A 92 N ASP A 46 SHEET 4 B 4 ILE A 108 ASP A 111 -1 O ILE A 110 N LEU A 91 SSBOND 1 CYS A 24 CYS A 77 1555 1555 2.03 SSBOND 2 CYS A 33 CYS A 97 1555 1555 2.03 CISPEP 1 LEU A 117 PRO A 118 0 8.69 CRYST1 70.321 33.368 49.265 90.00 106.83 90.00 C 1 2 1 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 0.014221 0.000000 0.004302 0.00000 SCALE2 0.000000 0.029969 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021207 0.00000