HEADER ANTIMICROBIAL PROTEIN 10-APR-17 5NNT TITLE THE DIMERIC STRUCTURE OF LL-37 CRYSTALLIZED IN DPC COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHELICIDIN ANTIMICROBIAL PEPTIDE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 18 KDA CATIONIC ANTIMICROBIAL PROTEIN,HCAP-18; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS AMP, LL-37, LDAO, PEPTIDE-DETERGENT COMPLEX, ANTIMICROBIAL PEPTIDE, KEYWDS 2 ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.ZETH,E.SANCHO-VAELLO REVDAT 2 16-OCT-19 5NNT 1 REMARK REVDAT 1 24-JAN-18 5NNT 0 JRNL AUTH E.SANCHO-VAELLO,P.FRANCOIS,E.J.BONETTI,H.LILIE,S.FINGER, JRNL AUTH 2 F.GIL-ORTIZ,D.GIL-CARTON,K.ZETH JRNL TITL STRUCTURAL REMODELING AND OLIGOMERIZATION OF HUMAN JRNL TITL 2 CATHELICIDIN ON MEMBRANES SUGGEST FIBRIL-LIKE STRUCTURES AS JRNL TITL 3 ACTIVE SPECIES. JRNL REF SCI REP V. 7 15371 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 29133814 JRNL DOI 10.1038/S41598-017-14206-1 REMARK 2 REMARK 2 RESOLUTION. 2.21 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) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 4433 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.264 REMARK 3 R VALUE (WORKING SET) : 0.263 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 223 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 29.5605 - 2.7826 0.99 2168 115 0.2392 0.2574 REMARK 3 2 2.7826 - 2.2089 0.97 2042 108 0.3264 0.3711 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.30 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 : 0.003 632 REMARK 3 ANGLE : 0.740 829 REMARK 3 CHIRALITY : 0.036 84 REMARK 3 PLANARITY : 0.003 96 REMARK 3 DIHEDRAL : 16.824 405 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.4996 15.4496 6.4826 REMARK 3 T TENSOR REMARK 3 T11: 0.4721 T22: 0.2128 REMARK 3 T33: 0.4313 T12: 0.2098 REMARK 3 T13: 0.0240 T23: 0.1708 REMARK 3 L TENSOR REMARK 3 L11: 5.7310 L22: 8.2766 REMARK 3 L33: 3.6668 L12: -0.1022 REMARK 3 L13: -0.7265 L23: 2.1617 REMARK 3 S TENSOR REMARK 3 S11: 0.0100 S12: -0.2533 S13: -0.4320 REMARK 3 S21: 0.2908 S22: 0.0572 S23: 0.3672 REMARK 3 S31: 0.1408 S32: -0.1314 S33: -0.1968 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 7 THROUGH 34 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.4605 -6.1254 4.0419 REMARK 3 T TENSOR REMARK 3 T11: 0.9370 T22: 0.0114 REMARK 3 T33: 0.2833 T12: -0.0966 REMARK 3 T13: -0.0570 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 1.1954 L22: 3.7248 REMARK 3 L33: 0.5650 L12: 1.2795 REMARK 3 L13: -0.5511 L23: -0.8972 REMARK 3 S TENSOR REMARK 3 S11: -0.1051 S12: 0.0602 S13: -0.0174 REMARK 3 S21: -0.3840 S22: 0.0280 S23: 0.2323 REMARK 3 S31: -0.0670 S32: 0.0114 S33: -0.0034 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 6 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.2411 -10.0029 8.9726 REMARK 3 T TENSOR REMARK 3 T11: 0.6800 T22: 0.2555 REMARK 3 T33: 0.7757 T12: 0.0441 REMARK 3 T13: 0.0005 T23: 0.0494 REMARK 3 L TENSOR REMARK 3 L11: 4.1987 L22: 5.4340 REMARK 3 L33: 3.2775 L12: 1.8030 REMARK 3 L13: 2.1303 L23: -1.5993 REMARK 3 S TENSOR REMARK 3 S11: -0.0838 S12: -0.2529 S13: 0.3619 REMARK 3 S21: 0.9788 S22: -0.0536 S23: -0.3126 REMARK 3 S31: -0.0756 S32: -0.0328 S33: 0.0583 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 7 THROUGH 33 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.1211 11.8639 7.0701 REMARK 3 T TENSOR REMARK 3 T11: 0.3367 T22: 0.2124 REMARK 3 T33: 0.3415 T12: 0.0264 REMARK 3 T13: -0.0492 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 1.2482 L22: 7.6931 REMARK 3 L33: 3.9688 L12: 0.0664 REMARK 3 L13: -0.1279 L23: 3.6513 REMARK 3 S TENSOR REMARK 3 S11: 0.0585 S12: 0.1434 S13: -0.1155 REMARK 3 S21: -0.8135 S22: 0.0477 S23: -0.8357 REMARK 3 S31: -0.1995 S32: 0.4304 S33: -0.1521 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 5NNT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-APR-17. REMARK 100 THE DEPOSITION ID IS D_1200004419. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-APR-13 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 : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4568 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0700 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 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEGMME 3350, 100 MM TRIS, PH 8, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 17.60450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.19900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.85150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.19900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.60450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.85150 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: 1560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 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 THR A 35 REMARK 465 GLU A 36 REMARK 465 SER A 37 REMARK 465 ARG B 34 REMARK 465 THR B 35 REMARK 465 GLU B 36 REMARK 465 SER B 37 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 ARG A 34 CG CD NE CZ NH1 NH2 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 LEU A 2 46.16 -143.74 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 DPV A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DPV B 101 DBREF 5NNT A 1 37 UNP P49913 CAMP_HUMAN 134 170 DBREF 5NNT B 1 37 UNP P49913 CAMP_HUMAN 134 170 SEQRES 1 A 37 LEU LEU GLY ASP PHE PHE ARG LYS SER LYS GLU LYS ILE SEQRES 2 A 37 GLY LYS GLU PHE LYS ARG ILE VAL GLN ARG ILE LYS ASP SEQRES 3 A 37 PHE LEU ARG ASN LEU VAL PRO ARG THR GLU SER SEQRES 1 B 37 LEU LEU GLY ASP PHE PHE ARG LYS SER LYS GLU LYS ILE SEQRES 2 B 37 GLY LYS GLU PHE LYS ARG ILE VAL GLN ARG ILE LYS ASP SEQRES 3 B 37 PHE LEU ARG ASN LEU VAL PRO ARG THR GLU SER HET DPV A 101 61 HET DPV B 101 61 HETNAM DPV DODECYL 2-(TRIMETHYLAMMONIO)ETHYL PHOSPHATE HETSYN DPV DODECYLPHOSPHOCHOLINE FORMUL 3 DPV 2(C17 H38 N O4 P) FORMUL 5 HOH *10(H2 O) HELIX 1 AA1 PHE A 6 VAL A 32 1 27 HELIX 2 AA2 PHE B 6 VAL B 32 1 27 SITE 1 AC1 4 PHE A 5 PHE A 6 GLU B 11 LYS B 15 SITE 1 AC2 5 GLN A 22 PHE B 5 PHE B 6 ASN B 30 SITE 2 AC2 5 HOH B 202 CRYST1 35.209 43.703 54.398 90.00 90.00 90.00 P 21 21 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 0.028402 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018383 0.00000