HEADER PLANT PROTEIN 30-APR-21 7MMY TITLE RACEMIC STRUCTURE OF THE CYCLIC PLANT PEPTIDE PDP-23 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PDP-23; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ZINNIA ELEGANS; SOURCE 4 ORGANISM_TAXID: 34245 KEYWDS PDP, HEAD-TO-TAIL CYCLIC, HOMODIMER, RACEMIC CRYSTALLOGRAPHY, PLANT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.VADLAMANI,C.S.BOND REVDAT 4 18-OCT-23 7MMY 1 REMARK REVDAT 3 19-JAN-22 7MMY 1 JRNL REVDAT 2 24-NOV-21 7MMY 1 JRNL REVDAT 1 12-MAY-21 7MMY 0 JRNL AUTH C.D.PAYNE,G.VADLAMANI,F.HAJIAGHAALIPOUR,T.MUHAMMAD, JRNL AUTH 2 M.F.FISHER,H.S.ANDERSSON,U.GORANSSON,R.J.CLARK,C.S.BOND, JRNL AUTH 3 J.S.MYLNE,K.J.ROSENGREN JRNL TITL SOLUTION NMR AND RACEMIC CRYSTALLOGRAPHY PROVIDE INSIGHTS JRNL TITL 2 INTO A NOVEL STRUCTURAL CLASS OF CYCLIC PLANT PEPTIDES. JRNL REF RSC CHEM BIOL V. 2 1682 2021 JRNL REFN ESSN 2633-0679 JRNL PMID 34977583 JRNL DOI 10.1039/D1CB00155H REMARK 2 REMARK 2 RESOLUTION. 1.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 13041 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.747 REMARK 3 FREE R VALUE TEST SET COUNT : 619 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.46 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.50 REMARK 3 REFLECTION IN BIN (WORKING SET) : 792 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.3550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 438 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.86700 REMARK 3 B22 (A**2) : -2.20900 REMARK 3 B33 (A**2) : 4.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.71900 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.073 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.055 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.514 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 513 ; 0.013 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 366 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 715 ; 1.822 ; 1.620 REMARK 3 BOND ANGLES OTHERS (DEGREES): 869 ; 1.664 ; 1.554 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 64 ; 8.137 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 24 ;35.360 ;22.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 49 ;10.299 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 57 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 610 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 126 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 94 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 65 ; 0.283 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 221 ; 0.200 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 28 ; 0.142 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 247 ; 3.263 ; 1.894 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 246 ; 3.251 ; 1.894 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 314 ; 3.858 ; 2.873 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 315 ; 3.854 ; 2.872 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 266 ; 5.108 ; 2.450 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 264 ; 4.999 ; 2.443 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 400 ; 5.811 ; 3.513 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 400 ; 5.669 ; 3.508 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 879 ; 8.917 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7MMY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-APR-21. REMARK 100 THE DEPOSITION ID IS D_1000255667. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13346 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.460 REMARK 200 RESOLUTION RANGE LOW (A) : 49.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 7L51 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 22.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE OBTAINED FROM A RACEMIC REMARK 280 MIX OF 7MG/ML EACH OF L- AND D-PEPTIDE IN 0.2 M TRIMETHYLAMINE N- REMARK 280 OXIDE DIHYDRATE, 0.1 M TRIS PH 8.5, 20% PEG MONOMETHYL ETHER REMARK 280 2000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21/n 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 3555 -X,-Y,-Z REMARK 290 4555 X+1/2,-Y+1/2,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 13.17762 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 24.50400 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 14.68932 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.17762 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.50400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.68932 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 HIS A 5 -101.08 56.66 REMARK 500 REMARK 500 REMARK: NULL DBREF 7MMY A 1 28 PDB 7MMY 7MMY 1 28 DBREF 7MMY B 1 28 PDB 7MMY 7MMY 1 28 SEQRES 1 A 28 GLY PHE CYS TRP HIS HIS SER CYS VAL PRO SER GLY THR SEQRES 2 A 28 CYS ALA ASP PHE PRO TRP PRO LEU GLY HIS GLN CYS PHE SEQRES 3 A 28 PRO ASP SEQRES 1 B 28 GLY PHE CYS TRP HIS HIS SER CYS VAL PRO SER GLY THR SEQRES 2 B 28 CYS ALA ASP PHE PRO TRP PRO LEU GLY HIS GLN CYS PHE SEQRES 3 B 28 PRO ASP FORMUL 3 HOH *45(H2 O) SHEET 1 AA1 2 PHE A 2 TRP A 4 0 SHEET 2 AA1 2 SER A 7 VAL A 9 -1 O SER A 7 N TRP A 4 SHEET 1 AA2 2 THR A 13 ASP A 16 0 SHEET 2 AA2 2 HIS A 23 PHE A 26 -1 O PHE A 26 N THR A 13 SHEET 1 AA3 2 PHE B 2 TRP B 4 0 SHEET 2 AA3 2 SER B 7 VAL B 9 -1 O VAL B 9 N PHE B 2 SHEET 1 AA4 2 THR B 13 ASP B 16 0 SHEET 2 AA4 2 HIS B 23 PHE B 26 -1 O PHE B 26 N THR B 13 SSBOND 1 CYS A 3 CYS A 8 1555 1555 2.00 SSBOND 2 CYS A 14 CYS A 25 1555 1555 2.02 SSBOND 3 CYS B 3 CYS B 8 1555 1555 2.03 SSBOND 4 CYS B 14 CYS B 25 1555 1555 2.04 LINK N GLY A 1 C ASP A 28 1555 1555 1.31 LINK N GLY B 1 C ASP B 28 1555 1555 1.34 CISPEP 1 TRP A 19 PRO A 20 0 4.87 CISPEP 2 TRP B 19 PRO B 20 0 12.05 CRYST1 27.527 49.008 29.402 90.00 92.28 90.00 P 1 21/n 1 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 0.036328 0.000000 0.001449 0.00000 SCALE2 0.000000 0.020405 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034038 0.00000