PDB Short entry for 5HPP HEADER DE NOVO PROTEIN 20-JAN-16 5HPP TITLE CRYSTAL STRUCTURE OF A MACROCYCLIC BETA-SHEET PEPTIDE DERIVED FROM TITLE 2 TRANSTHYRETIN (106-121) - (ORN)TIA(MAA)LLS(ORN)S(PHI)STTAV COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORN-THR-ILE-ALA-MAA-LEU-LEU-SER-ORN-SER-PHI-SER-THR-THR- COMPND 3 ALA-VAL; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS BETA-HAIRPIN, NANOTUBE ASSEMBLY, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.YOO,A.G.KREUTZER,J.S.NOWICK REVDAT 4 25-DEC-19 5HPP 1 REMARK REVDAT 3 20-SEP-17 5HPP 1 REMARK REVDAT 2 17-MAY-17 5HPP 1 JRNL REVDAT 1 10-AUG-16 5HPP 0 JRNL AUTH S.YOO,A.G.KREUTZER,N.L.TRUEX,J.S.NOWICK JRNL TITL SQUARE CHANNELS FORMED BY A PEPTIDE DERIVED FROM JRNL TITL 2 TRANSTHYRETIN. JRNL REF CHEM SCI V. 7 6946 2016 JRNL REFN ISSN 2041-6520 JRNL PMID 28451128 JRNL DOI 10.1039/C6SC01927G REMARK 2 REMARK 2 RESOLUTION. 2.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: 000) 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) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 1700 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.120 REMARK 3 FREE R VALUE TEST SET COUNT : 172 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 21.1500 - 2.0818 1.00 1528 172 0.1593 0.1839 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 10.230 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 : 0.006 115 REMARK 3 ANGLE : 0.971 155 REMARK 3 CHIRALITY : 0.047 23 REMARK 3 PLANARITY : 0.004 17 REMARK 3 DIHEDRAL : 27.281 78 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.2569 26.7672 7.6429 REMARK 3 T TENSOR REMARK 3 T11: 0.1397 T22: 0.0909 REMARK 3 T33: 0.1328 T12: -0.0016 REMARK 3 T13: -0.0195 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 0.6076 L22: 2.3002 REMARK 3 L33: 3.7037 L12: 0.7292 REMARK 3 L13: -1.2306 L23: -2.5154 REMARK 3 S TENSOR REMARK 3 S11: -0.0806 S12: 0.0185 S13: -0.0986 REMARK 3 S21: 0.1317 S22: 0.1887 S23: 0.1426 REMARK 3 S31: 0.2714 S32: -0.1213 S33: -0.0560 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 5HPP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000217497. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 133 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-003 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : CU REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM 7.2.1 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2053 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.082 REMARK 200 RESOLUTION RANGE LOW (A) : 21.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.04945 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.11010 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.490 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER (1.10.1_2155: 000) REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THIN ELONGATED RODS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NAOAC PH 5.3, 0.2 M CACL2, AND REMARK 280 31% ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 8.16000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 21.15000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 21.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 12.24000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 21.15000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 21.15000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 4.08000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 21.15000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 21.15000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 12.24000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 21.15000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 21.15000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 4.08000 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 8.16000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 16.32000 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 CL CL A 101 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 207 O HOH A 212 2.05 REMARK 500 O HOH A 205 O HOH A 209 2.08 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 Ligand residues ORN A 9 through REMARK 800 SER A 10 bound to SER A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues PHI A 11 REMARK 800 through SER A 12 bound to SER A 10 DBREF 5HPP A 1 16 PDB 5HPP 5HPP 1 16 SEQRES 1 A 16 ORN THR ILE ALA MAA LEU LEU SER ORN SER PHI SER THR SEQRES 2 A 16 THR ALA VAL HET ORN A 1 19 HET MAA A 5 13 HET ORN A 9 19 HET PHI A 11 20 HET CL A 101 1 HETNAM ORN L-ORNITHINE HETNAM MAA N-METHYL-L-ALANINE HETNAM PHI IODO-PHENYLALANINE HETNAM CL CHLORIDE ION FORMUL 1 ORN 2(C5 H12 N2 O2) FORMUL 1 MAA C4 H9 N O2 FORMUL 1 PHI C9 H10 I N O2 FORMUL 2 CL CL 1- FORMUL 3 HOH *14(H2 O) SHEET 1 AA1 2 THR A 2 LEU A 7 0 SHEET 2 AA1 2 PHI A 11 VAL A 16 -1 O SER A 12 N LEU A 6 LINK NE ORN A 1 C VAL A 16 1555 1555 1.38 LINK C ORN A 1 N THR A 2 1555 1555 1.37 LINK C ALA A 4 N MAA A 5 1555 1555 1.34 LINK C MAA A 5 N LEU A 6 1555 1555 1.33 LINK C SER A 8 NE ORN A 9 1555 1555 1.38 LINK C ORN A 9 N SER A 10 1555 1555 1.37 LINK C SER A 10 N PHI A 11 1555 1555 1.29 LINK C PHI A 11 N SER A 12 1555 1555 1.33 SITE 1 AC1 10 ORN A 1 THR A 2 ILE A 3 LEU A 7 SITE 2 AC1 10 SER A 8 PHI A 11 THR A 13 HOH A 201 SITE 3 AC1 10 HOH A 207 HOH A 208 SITE 1 AC2 7 ORN A 1 ILE A 3 MAA A 5 LEU A 6 SITE 2 AC2 7 SER A 10 THR A 13 HOH A 212 CRYST1 42.300 42.300 16.320 90.00 90.00 90.00 P 43 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 0.023641 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023641 0.000000 0.00000 SCALE3 0.000000 0.000000 0.061275 0.00000 HETATM 1 N ORN A 1 39.331 34.052 -2.878 1.00 13.84 N1+ ANISOU 1 N ORN A 1 1500 1862 1898 -38 -333 -141 N1+ HETATM 2 CA ORN A 1 38.103 33.457 -2.305 1.00 11.11 C ANISOU 2 CA ORN A 1 1162 1493 1564 -74 -351 -133 C HETATM 3 CB ORN A 1 37.998 31.967 -2.694 1.00 21.96 C ANISOU 3 CB ORN A 1 2597 2797 2949 -106 -400 -170 C HETATM 4 CG ORN A 1 37.683 31.705 -4.172 1.00 24.59 C ANISOU 4 CG ORN A 1 2976 3116 3252 -194 -403 -189 C HETATM 5 CD ORN A 1 36.266 32.135 -4.590 1.00 24.35 C ANISOU 5 CD ORN A 1 2896 3159 3195 -279 -371 -132 C HETATM 6 NE ORN A 1 35.227 31.306 -3.990 1.00 16.64 N ANISOU 6 NE ORN A 1 1947 2157 2217 -353 -396 -83 N HETATM 7 C ORN A 1 38.119 33.572 -0.781 1.00 12.41 C ANISOU 7 C ORN A 1 1329 1649 1738 -39 -368 -123 C HETATM 8 O ORN A 1 39.130 33.913 -0.168 1.00 10.22 O ANISOU 8 O ORN A 1 1057 1387 1440 -5 -377 -123 O HETATM 9 H2 ORN A 1 39.268 34.220 -3.885 1.00 16.61 H1+ HETATM 10 H ORN A 1 39.572 34.957 -2.466 1.00 16.61 H1+ HETATM 11 H3 ORN A 1 40.160 33.467 -2.751 1.00 16.61 H1+ HETATM 12 HA ORN A 1 37.269 34.058 -2.680 1.00 13.33 H HETATM 13 HB2 ORN A 1 38.935 31.451 -2.442 1.00 26.35 H HETATM 14 HB3 ORN A 1 37.167 31.538 -2.117 1.00 26.35 H HETATM 15 HG2 ORN A 1 37.788 30.631 -4.364 1.00 29.51 H HETATM 16 HG3 ORN A 1 38.413 32.242 -4.789 1.00 29.51 H HETATM 17 HD2 ORN A 1 36.188 32.045 -5.678 1.00 29.22 H HETATM 18 HD3 ORN A 1 36.110 33.172 -4.280 1.00 29.22 H HETATM 19 HE1 ORN A 1 34.893 30.531 -4.560 1.00 19.96 H