HEADER ANTIBIOTIC 17-MAY-22 8CUG TITLE SYNTHETIC EPI-NOVO29 (2R,3S), SYNCHROTRON STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNTHETIC EPI-NOVO29 (2R,3S); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ELEFTHERIA; SOURCE 4 ORGANISM_TAXID: 1597779 KEYWDS MACROCYCLIC PEPTIDE, ANTIBIOTIC EXPDTA X-RAY DIFFRACTION AUTHOR A.G.KREUTZER,X.LI,M.KRUMBERGER,J.S.NOWICK REVDAT 5 15-NOV-23 8CUG 1 LINK ATOM REVDAT 4 25-OCT-23 8CUG 1 REMARK REVDAT 3 01-MAR-23 8CUG 1 JRNL REVDAT 2 01-FEB-23 8CUG 1 JRNL REVDAT 1 11-JAN-23 8CUG 0 JRNL AUTH M.KRUMBERGER,X.LI,A.G.KREUTZER,A.J.PEOPLES,A.G.NITTI, JRNL AUTH 2 A.M.CUNNINGHAM,C.R.JONES,C.ACHORN,L.L.LING,D.E.HUGHES, JRNL AUTH 3 J.S.NOWICK JRNL TITL SYNTHESIS AND STEREOCHEMICAL DETERMINATION OF THE PEPTIDE JRNL TITL 2 ANTIBIOTIC NOVO29. JRNL REF J.ORG.CHEM. V. 88 2214 2023 JRNL REFN ISSN 0022-3263 JRNL PMID 36655882 JRNL DOI 10.1021/ACS.JOC.2C02648 REMARK 2 REMARK 2 RESOLUTION. 1.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.450 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 9930 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.145 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 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 24.1900 - 2.1600 1.00 1338 145 0.1136 0.1359 REMARK 3 2 2.1600 - 1.7200 1.00 1325 149 0.1174 0.1344 REMARK 3 3 1.7200 - 1.5000 1.00 1330 144 0.1346 0.1561 REMARK 3 4 1.5000 - 1.3600 1.00 1330 143 0.1397 0.1275 REMARK 3 5 1.3600 - 1.2700 1.00 1342 146 0.1330 0.1368 REMARK 3 6 1.2700 - 1.1900 0.98 1305 147 0.1874 0.2004 REMARK 3 7 1.1900 - 1.1310 0.73 972 114 0.2285 0.2350 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 17.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.98 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 : NULL 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 8CUG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265477. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 143 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL, SI(111) 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9930 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.131 REMARK 200 RESOLUTION RANGE LOW (A) : 24.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.07324 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32040 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: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 8CUF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8 M SODIUM ACETATE TRIHYDRATE, PH REMARK 280 6.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296.15K 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 6.05250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.55050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.94900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 18.55050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 6.05250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.94900 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 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 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 211 O HOH A 215 1.78 REMARK 500 O HOH A 212 O HOH A 214 1.80 REMARK 500 O HOH B 112 O HOH B 114 1.88 REMARK 500 O HOH B 101 O HOH B 119 2.03 REMARK 500 O HOH A 212 O HOH A 213 2.06 REMARK 500 O SER A 4 O HOH A 201 2.15 REMARK 500 O HOH B 108 O HOH B 118 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 201 O HOH B 103 1655 1.71 REMARK 500 O HOH A 214 O HOH B 103 1655 1.75 REMARK 500 O HOH A 205 O HOH A 216 3655 1.90 REMARK 500 O HOH A 216 O HOH B 112 1655 1.91 REMARK 500 O HOH A 215 O HOH B 110 1655 2.01 REMARK 500 REMARK 500 REMARK: NULL DBREF 8CUG A 1 8 PDB 8CUG 8CUG 1 8 DBREF 8CUG B 1 8 PDB 8CUG 8CUG 1 8 SEQRES 1 A 8 PHE DLE DLY SER OWF ALA LEU LEU SEQRES 1 B 8 PHE DLE DLY SER OWF ALA LEU LEU HET DLE A 2 19 HET DLY A 3 22 HET OWF A 5 14 HET DLE B 2 19 HET DLY B 3 22 HET OWF B 5 14 HET ACT A 101 7 HETNAM DLE D-LEUCINE HETNAM DLY D-LYSINE HETNAM OWF (3S)-3-HYDROXY-D-ASPARAGINE HETNAM ACT ACETATE ION FORMUL 1 DLE 2(C6 H13 N O2) FORMUL 1 DLY 2(C6 H14 N2 O2) FORMUL 1 OWF 2(C4 H8 N2 O4) FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HOH *42(H2 O) LINK C PHE A 1 N DLE A 2 1555 1555 1.32 LINK C DLE A 2 N DLY A 3 1555 1555 1.33 LINK C DLY A 3 N SER A 4 1555 1555 1.33 LINK C SER A 4 N OWF A 5 1555 1555 1.34 LINK C OWF A 5 N ALA A 6 1555 1555 1.33 LINK OB1 OWF A 5 C LEU A 8 1555 1555 1.36 LINK C PHE B 1 N DLE B 2 1555 1555 1.33 LINK C DLE B 2 N DLY B 3 1555 1555 1.33 LINK C DLY B 3 N SER B 4 1555 1555 1.33 LINK C SER B 4 N OWF B 5 1555 1555 1.33 LINK C OWF B 5 N ALA B 6 1555 1555 1.32 LINK OB1 OWF B 5 C LEU B 8 1555 1555 1.36 CRYST1 12.105 31.898 37.101 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 0.082610 0.000000 0.000000 0.00000 SCALE2 0.000000 0.031350 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026953 0.00000