HEADER PLANT PROTEIN 20-JUL-21 7RIJ TITLE [I11G]HYEN D COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLOTIDE HYEN-D; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: D-[I11L]HYEN D; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HYBANTHUS ENNEASPERMUS; SOURCE 4 ORGANISM_COMMON: SPADE FLOWER, VIOLA ENNEASPERMA; SOURCE 5 ORGANISM_TAXID: 212266; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HYBANTHUS ENNEASPERMUS; SOURCE 9 ORGANISM_TAXID: 212266 KEYWDS CYTOTOXICITY, CYCLOTIDES, QUASI-RACEMIC CRYSTALLOGRAPHY, PLANT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Q.DU,Y.H.HUANG,C.K.WANG,D.J.CRAIK REVDAT 5 13-NOV-24 7RIJ 1 REMARK REVDAT 4 15-NOV-23 7RIJ 1 REMARK REVDAT 3 18-OCT-23 7RIJ 1 REMARK REVDAT 2 29-SEP-21 7RIJ 1 JRNL REVDAT 1 22-SEP-21 7RIJ 0 JRNL AUTH D.J.CRAIK,Y.H.HUANG,C.K.WANG,Q.DU,G.KING JRNL TITL ENABLING EFFICIENT FOLDING AND HIGH-RESOLUTION JRNL TITL 2 CRYSTALLOGRAPHIC ANALYSIS OF BRACELET CYCLOTIDES JRNL REF MOLECULES V.(18) 5554 2021 JRNL REFN ESSN 1420-3049 JRNL DOI 10.3390/MOLECULES26185554 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.040 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 9731 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.150 REMARK 3 FREE R VALUE TEST SET COUNT : 988 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 21.6300 - 2.4900 0.97 1305 146 0.1489 0.1615 REMARK 3 2 2.4900 - 1.9700 0.95 1252 146 0.1411 0.1538 REMARK 3 3 1.9700 - 1.7200 0.95 1267 135 0.1452 0.1645 REMARK 3 4 1.7200 - 1.5700 0.94 1267 144 0.1423 0.1671 REMARK 3 5 1.5700 - 1.4500 0.93 1218 140 0.1422 0.1657 REMARK 3 6 1.4500 - 1.3700 0.93 1236 140 0.1491 0.1451 REMARK 3 7 1.3700 - 1.3000 0.89 1198 137 0.1627 0.1952 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.74 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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): 11.2842 -7.2974 -3.5397 REMARK 3 T TENSOR REMARK 3 T11: 0.0373 T22: 0.0273 REMARK 3 T33: 0.0470 T12: -0.0059 REMARK 3 T13: -0.0020 T23: -0.0116 REMARK 3 L TENSOR REMARK 3 L11: 1.1410 L22: 1.4870 REMARK 3 L33: 2.2983 L12: -0.6305 REMARK 3 L13: 0.3442 L23: -0.9206 REMARK 3 S TENSOR REMARK 3 S11: -0.0254 S12: -0.0060 S13: 0.0282 REMARK 3 S21: -0.0089 S22: 0.0210 S23: -0.0156 REMARK 3 S31: -0.0018 S32: 0.0349 S33: 0.0043 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 7RIJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000256362. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-20 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976255 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9744 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 21.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.02900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.04700 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: 7RII REMARK 200 REMARK 200 REMARK: ROD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 %W/V PEG 3350 (POLYMER) 0.2 M REMARK 280 CA(OAC)2 (SALT), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 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 CYS A 8 44.08 -140.82 REMARK 500 DCY B 8 -46.59 143.48 REMARK 500 DLY B 25 -5.47 -81.60 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 232 DISTANCE = 8.86 ANGSTROMS REMARK 525 HOH B 335 DISTANCE = 7.14 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7RIH RELATED DB: PDB REMARK 900 RELATED ID: 7RII RELATED DB: PDB DBREF 7RIJ A 1 30 UNP C0HLN8 CYHED_HYBEN 1 30 DBREF 7RIJ B 1 30 PDB 7RIJ 7RIJ 1 30 SEQADV 7RIJ GLY A 11 UNP C0HLN8 ILE 11 ENGINEERED MUTATION SEQRES 1 A 30 GLY PHE PRO CYS GLY GLU SER CYS VAL TYR GLY PRO CYS SEQRES 2 A 30 PHE THR ALA ALA ILE GLY CYS SER CYS LYS SER LYS VAL SEQRES 3 A 30 CYS TYR LYS ASN SEQRES 1 B 30 GLY DPN DPR DCY GLY DGL DSN DCY DVA DTY DLE DPR DCY SEQRES 2 B 30 DPN DTH DAL DAL DIL GLY DCY DSN DCY DLY DSN DLY DVA SEQRES 3 B 30 DCY DTY DLY DSG HET DPN B 2 20 HET DPR B 3 14 HET DCY B 4 10 HET DGL B 6 15 HET DSN B 7 11 HET DCY B 8 10 HET DVA B 9 16 HET DTY B 10 21 HET DLE B 11 19 HET DPR B 12 14 HET DCY B 13 10 HET DPN B 14 20 HET DTH B 15 14 HET DAL B 16 7 HET DAL B 17 10 HET DIL B 18 19 HET DCY B 20 10 HET DSN B 21 11 HET DCY B 22 10 HET DLY B 23 19 HET DSN B 24 11 HET DLY B 25 21 HET DVA B 26 16 HET DCY B 27 10 HET DTY B 28 21 HET DLY B 29 21 HET DSG B 30 14 HET ACT A 101 7 HET ACT A 102 7 HET ACT B 201 7 HETNAM DPN D-PHENYLALANINE HETNAM DPR D-PROLINE HETNAM DCY D-CYSTEINE HETNAM DGL D-GLUTAMIC ACID HETNAM DSN D-SERINE HETNAM DVA D-VALINE HETNAM DTY D-TYROSINE HETNAM DLE D-LEUCINE HETNAM DTH D-THREONINE HETNAM DAL D-ALANINE HETNAM DIL D-ISOLEUCINE HETNAM DLY D-LYSINE HETNAM DSG D-ASPARAGINE HETNAM ACT ACETATE ION FORMUL 2 DPN 2(C9 H11 N O2) FORMUL 2 DPR 2(C5 H9 N O2) FORMUL 2 DCY 6(C3 H7 N O2 S) FORMUL 2 DGL C5 H9 N O4 FORMUL 2 DSN 3(C3 H7 N O3) FORMUL 2 DVA 2(C5 H11 N O2) FORMUL 2 DTY 2(C9 H11 N O3) FORMUL 2 DLE C6 H13 N O2 FORMUL 2 DTH C4 H9 N O3 FORMUL 2 DAL 2(C3 H7 N O2) FORMUL 2 DIL C6 H13 N O2 FORMUL 2 DLY 3(C6 H14 N2 O2) FORMUL 2 DSG C4 H8 N2 O3 FORMUL 3 ACT 3(C2 H3 O2 1-) FORMUL 6 HOH *67(H2 O) HELIX 1 AA1 CYS A 13 GLY A 19 5 7 HELIX 2 AA2 DCY B 13 GLY B 19 5 7 SHEET 1 AA1 3 PHE A 2 SER A 7 0 SHEET 2 AA1 3 VAL A 26 LYS A 29 -1 O CYS A 27 N GLU A 6 SHEET 3 AA1 3 SER A 21 LYS A 23 -1 N LYS A 23 O VAL A 26 SHEET 1 AA2 3 DPN B 2 DSN B 7 0 SHEET 2 AA2 3 DVA B 26 DLY B 29 -1 O DCY B 27 N DCY B 4 SHEET 3 AA2 3 DSN B 21 DLY B 23 -1 N DLY B 23 O DVA B 26 SSBOND 1 CYS A 4 CYS A 20 1555 1555 2.04 SSBOND 2 CYS A 8 CYS A 22 1555 1555 2.04 SSBOND 3 CYS A 13 CYS A 27 1555 1555 2.03 SSBOND 4 DCY B 4 DCY B 20 1555 1555 2.04 SSBOND 5 DCY B 8 DCY B 22 1555 1555 2.04 SSBOND 6 DCY B 13 DCY B 27 1555 1555 2.04 LINK N GLY A 1 C ASN A 30 1555 1555 1.33 LINK C GLY B 1 N DPN B 2 1555 1555 1.33 LINK N GLY B 1 C DSG B 30 1555 1555 1.30 LINK C DPN B 2 N DPR B 3 1555 1555 1.35 LINK C DPR B 3 N DCY B 4 1555 1555 1.33 LINK C DCY B 4 N GLY B 5 1555 1555 1.33 LINK C GLY B 5 N DGL B 6 1555 1555 1.33 LINK C DGL B 6 N DSN B 7 1555 1555 1.33 LINK C DSN B 7 N DCY B 8 1555 1555 1.33 LINK C DCY B 8 N DVA B 9 1555 1555 1.33 LINK C DVA B 9 N DTY B 10 1555 1555 1.33 LINK C DTY B 10 N DLE B 11 1555 1555 1.32 LINK C DLE B 11 N DPR B 12 1555 1555 1.34 LINK C DPR B 12 N DCY B 13 1555 1555 1.32 LINK C DCY B 13 N DPN B 14 1555 1555 1.34 LINK C DPN B 14 N DTH B 15 1555 1555 1.33 LINK C DTH B 15 N DAL B 16 1555 1555 1.33 LINK C DAL B 16 N DAL B 17 1555 1555 1.33 LINK C DAL B 17 N DIL B 18 1555 1555 1.33 LINK C DIL B 18 N GLY B 19 1555 1555 1.33 LINK C GLY B 19 N DCY B 20 1555 1555 1.33 LINK C DCY B 20 N DSN B 21 1555 1555 1.33 LINK C DSN B 21 N DCY B 22 1555 1555 1.32 LINK C DCY B 22 N DLY B 23 1555 1555 1.33 LINK C DLY B 23 N DSN B 24 1555 1555 1.33 LINK C DSN B 24 N DLY B 25 1555 1555 1.33 LINK C DLY B 25 N DVA B 26 1555 1555 1.34 LINK C DVA B 26 N DCY B 27 1555 1555 1.33 LINK C DCY B 27 N DTY B 28 1555 1555 1.34 LINK C DTY B 28 N DLY B 29 1555 1555 1.32 LINK C DLY B 29 N DSG B 30 1555 1555 1.33 CRYST1 22.655 23.850 24.246 65.58 66.17 76.03 P 1 1 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 0.044140 -0.010978 -0.016678 0.00000 SCALE2 0.000000 0.043206 -0.016451 0.00000 SCALE3 0.000000 0.000000 0.048245 0.00000