HEADER IMMUNE SYSTEM 23-DEC-15 5H8D TITLE CRYSTAL STRUCTURE OF AN ASC BINDING NANOBODY COMPND MOL_ID: 1; COMPND 2 MOLECULE: VHH NANOBODY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_COMMON: LLAMA; SOURCE 4 ORGANISM_TAXID: 9844; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VHH NANOBODY, ASC-BINDING, ANTIBODY FRAGMENT, INFLAMMASOME, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.LU,F.I.SCHMIDT,J.RUAN,C.TANG,H.WU,H.L.PLOEGH REVDAT 4 06-NOV-24 5H8D 1 JRNL REMARK REVDAT 3 18-MAY-16 5H8D 1 JRNL REVDAT 2 27-APR-16 5H8D 1 JRNL REVDAT 1 06-APR-16 5H8D 0 JRNL AUTH F.I.SCHMIDT,A.LU,J.W.CHEN,J.RUAN,C.TANG,H.WU,H.L.PLOEGH JRNL TITL A SINGLE DOMAIN ANTIBODY FRAGMENT THAT RECOGNIZES THE JRNL TITL 2 ADAPTOR ASC DEFINES THE ROLE OF ASC DOMAINS IN INFLAMMASOME JRNL TITL 3 ASSEMBLY. JRNL REF J.EXP.MED. V. 213 771 2016 JRNL REFN ESSN 1540-9538 JRNL PMID 27069117 JRNL DOI 10.1084/JEM.20151790 REMARK 2 REMARK 2 RESOLUTION. 1.89 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) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.460 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 12735 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1274 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 68.9328 - 3.9300 1.00 1395 155 0.1490 0.1688 REMARK 3 2 3.9300 - 3.1194 1.00 1313 146 0.1672 0.1765 REMARK 3 3 3.1194 - 2.7250 1.00 1289 144 0.1931 0.2463 REMARK 3 4 2.7250 - 2.4759 1.00 1262 140 0.1846 0.2564 REMARK 3 5 2.4759 - 2.2984 1.00 1266 141 0.1829 0.2135 REMARK 3 6 2.2984 - 2.1629 1.00 1261 140 0.1654 0.2134 REMARK 3 7 2.1629 - 2.0546 1.00 1265 140 0.1698 0.2387 REMARK 3 8 2.0546 - 1.9651 0.99 1234 138 0.1628 0.1963 REMARK 3 9 1.9651 - 1.8900 0.94 1176 130 0.1682 0.2056 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.17 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 : 0.006 880 REMARK 3 ANGLE : 0.967 1185 REMARK 3 CHIRALITY : 0.047 122 REMARK 3 PLANARITY : 0.004 154 REMARK 3 DIHEDRAL : 12.821 313 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -29.2134 10.7299 4.4430 REMARK 3 T TENSOR REMARK 3 T11: 0.1251 T22: 0.1482 REMARK 3 T33: 0.1205 T12: -0.0006 REMARK 3 T13: 0.0191 T23: 0.0260 REMARK 3 L TENSOR REMARK 3 L11: 2.0139 L22: 4.4696 REMARK 3 L33: 1.7168 L12: -0.6631 REMARK 3 L13: -0.1559 L23: 1.2971 REMARK 3 S TENSOR REMARK 3 S11: 0.1071 S12: 0.1668 S13: 0.0199 REMARK 3 S21: -0.0628 S22: -0.1528 S23: -0.0908 REMARK 3 S31: 0.0238 S32: -0.1324 S33: 0.0306 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 5H8D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000216658. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12777 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 68.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID AT PH 3.5 AND 35% REMARK 280 PEG3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 15.94050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 48.71050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.71050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 7.97025 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.71050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 48.71050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 23.91075 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 48.71050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.71050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 7.97025 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 48.71050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.71050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 23.91075 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 15.94050 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 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 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 233 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 318 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 HOH A 274 O HOH A 288 2.11 REMARK 500 O HOH A 287 O HOH A 297 2.19 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 SER A 87 51.84 38.75 REMARK 500 ALA A 94 166.12 179.39 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 327 DISTANCE = 6.17 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5H8O RELATED DB: PDB DBREF 5H8D A 3 116 PDB 5H8D 5H8D 3 116 SEQRES 1 A 114 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 114 PRO GLY GLY SER LEU LYS LEU SER CYS ALA ALA SER GLY SEQRES 3 A 114 PHE THR PHE SER ARG TYR ALA MET SER TRP TYR ARG GLN SEQRES 4 A 114 ALA PRO GLY LYS GLU ARG GLU SER VAL ALA ARG ILE SER SEQRES 5 A 114 SER GLY GLY GLY THR ILE TYR TYR ALA ASP SER VAL LYS SEQRES 6 A 114 GLY ARG PHE THR ILE SER ARG GLU ASP ALA LYS ASN THR SEQRES 7 A 114 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 A 114 ALA VAL TYR TYR CYS TYR VAL GLY GLY PHE TRP GLY GLN SEQRES 9 A 114 GLY THR GLN VAL THR VAL SER SER GLY GLY FORMUL 2 HOH *127(H2 O) HELIX 1 AA1 THR A 30 TYR A 34 5 5 HELIX 2 AA2 ASP A 64 LYS A 67 5 4 HELIX 3 AA3 ASP A 76 LYS A 78 5 3 HELIX 4 AA4 LYS A 89 THR A 93 5 5 SHEET 1 AA1 4 GLN A 5 SER A 9 0 SHEET 2 AA1 4 LEU A 20 SER A 27 -1 O ALA A 25 N GLN A 7 SHEET 3 AA1 4 THR A 80 MET A 85 -1 O MET A 85 N LEU A 20 SHEET 4 AA1 4 PHE A 70 GLU A 75 -1 N SER A 73 O TYR A 82 SHEET 1 AA2 6 GLY A 12 VAL A 14 0 SHEET 2 AA2 6 THR A 108 VAL A 112 1 O THR A 111 N GLY A 12 SHEET 3 AA2 6 ALA A 94 VAL A 100 -1 N TYR A 96 O THR A 108 SHEET 4 AA2 6 MET A 36 GLN A 41 -1 N TYR A 39 O TYR A 97 SHEET 5 AA2 6 GLU A 48 ILE A 53 -1 O GLU A 48 N ARG A 40 SHEET 6 AA2 6 ILE A 60 TYR A 62 -1 O TYR A 61 N ARG A 52 SHEET 1 AA3 4 GLY A 12 VAL A 14 0 SHEET 2 AA3 4 THR A 108 VAL A 112 1 O THR A 111 N GLY A 12 SHEET 3 AA3 4 ALA A 94 VAL A 100 -1 N TYR A 96 O THR A 108 SHEET 4 AA3 4 PHE A 103 TRP A 104 -1 O PHE A 103 N VAL A 100 SSBOND 1 CYS A 24 CYS A 98 1555 1555 2.05 CRYST1 97.421 97.421 31.881 90.00 90.00 90.00 P 41 21 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 0.010265 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010265 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031367 0.00000