HEADER UNKNOWN FUNCTION 13-MAY-21 7ETP TITLE CRYSTAL STRUCTURE OF PRO-PHE-LEU-PHE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRO-PHE-LEU-PHE; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS SYNTHETIC PEPTIDE, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.KURUMIDA,K.IKEDA,Y.NAKAMICHI,A.HIRANO,K.KOBAYASHI,Y.SAITO,T.KAMEDA REVDAT 1 18-MAY-22 7ETP 0 JRNL AUTH Y.KURUMIDA,K.IKEDA,Y.NAKAMICHI,A.HIRANO,K.KOBAYASHI,Y.SAITO, JRNL AUTH 2 T.KAMEDA JRNL TITL CRYSTAL STRUCTURE OF PRO-PHE-LEU-PHE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12 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) : 1.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 4366 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 218 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 21.4600 - 2.1900 1.00 584 31 0.1125 0.1262 REMARK 3 2 2.1900 - 1.7400 1.00 535 28 0.1173 0.1372 REMARK 3 3 1.7400 - 1.5200 0.99 514 28 0.1501 0.1380 REMARK 3 4 1.5200 - 1.3800 1.00 501 26 0.1773 0.1732 REMARK 3 5 1.3800 - 1.2800 1.00 532 28 0.2002 0.1803 REMARK 3 6 1.2800 - 1.2100 0.99 485 26 0.2472 0.2817 REMARK 3 7 1.2100 - 1.1400 0.98 521 26 0.3467 0.4701 REMARK 3 8 1.1400 - 1.0900 0.97 476 25 0.3708 0.4981 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.72 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.40 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 : 0.009 129 REMARK 3 ANGLE : 1.224 173 REMARK 3 CHIRALITY : 1.246 17 REMARK 3 PLANARITY : 0.006 20 REMARK 3 DIHEDRAL : 14.830 43 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): -0.3630 -3.7438 -7.6113 REMARK 3 T TENSOR REMARK 3 T11: 0.0765 T22: 0.0808 REMARK 3 T33: 0.0875 T12: 0.0086 REMARK 3 T13: -0.0081 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 2.7678 L22: 1.9974 REMARK 3 L33: 4.8232 L12: 0.4729 REMARK 3 L13: -1.5496 L23: -1.0660 REMARK 3 S TENSOR REMARK 3 S11: -0.0161 S12: 0.0074 S13: -0.0322 REMARK 3 S21: -0.0446 S22: -0.0245 S23: -0.0053 REMARK 3 S31: 0.0486 S32: -0.0168 S33: 0.0432 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 7ETP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1300022207. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4389 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.095 REMARK 200 RESOLUTION RANGE LOW (A) : 42.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.925 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.74 REMARK 200 R MERGE FOR SHELL (I) : 1.14200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.330 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 20.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MOPS, 5 MM EDTA-2NA, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 4.81550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.46000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 11.78750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.46000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 4.81550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 11.78750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 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 B 103 DISTANCE = 6.34 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7ETN RELATED DB: PDB DBREF 7ETP A 1 4 PDB 7ETP 7ETP 1 4 DBREF 7ETP B 54 57 PDB 7ETP 7ETP 54 57 DBREF 7ETP C 1 4 PDB 7ETP 7ETP 1 4 SEQRES 1 A 4 PRO PHE LEU PHE SEQRES 1 B 4 PRO PHE LEU PHE SEQRES 1 C 4 PRO PHE LEU PHE FORMUL 4 HOH *10(H2 O) SHEET 1 AA1 2 PHE A 2 LEU A 3 0 SHEET 2 AA1 2 PHE B 55 LEU B 56 -1 O PHE B 55 N LEU A 3 CRYST1 9.631 23.575 42.920 90.00 90.00 90.00 P 21 21 21 12 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 0.103831 0.000000 0.000000 0.00000 SCALE2 0.000000 0.042418 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023299 0.00000