HEADER UNKNOWN FUNCTION 14-AUG-17 5OQZ TITLE CRYSTAL STRUCTURE OF THE LASSO PEPTIDE RUBRIVINODIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUBRIVINODIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 21-38; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: ISOPEPTIDE BOND BETWEEN GLY1N AND GLU9CD SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RUBRIVIVAX GELATINOSUS IL144; SOURCE 3 ORGANISM_TAXID: 983917; SOURCE 4 GENE: RGE_06990; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS LASSO PEPTIDE, RIBOSOMALLY SYNTHESIZED AND POST-TRANSLATIONALLY KEYWDS 2 MODIFIED PEPTIDE, RIPP, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR C.D.FAGE,J.D.HEGEMANN,M.A.MARAHIEL REVDAT 6 08-MAY-24 5OQZ 1 REMARK REVDAT 5 16-OCT-19 5OQZ 1 REMARK REVDAT 4 08-MAY-19 5OQZ 1 REMARK LINK REVDAT 3 07-MAR-18 5OQZ 1 JRNL REVDAT 2 14-FEB-18 5OQZ 1 JRNL REVDAT 1 07-FEB-18 5OQZ 0 JRNL AUTH K.JEANNE DIT FOUQUE,H.LAVANANT,S.ZIRAH,J.D.HEGEMANN, JRNL AUTH 2 C.D.FAGE,M.A.MARAHIEL,S.REBUFFAT,C.AFONSO JRNL TITL GENERAL RULES OF FRAGMENTATION EVIDENCING LASSO STRUCTURES JRNL TITL 2 IN CID AND ETD. JRNL REF ANALYST V. 143 1157 2018 JRNL REFN ISSN 1364-5528 JRNL PMID 29404537 JRNL DOI 10.1039/C7AN02052J REMARK 2 REMARK 2 RESOLUTION. 0.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 0.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.7 REMARK 3 NUMBER OF REFLECTIONS : 9038 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.085 REMARK 3 R VALUE (WORKING SET) : 0.084 REMARK 3 FREE R VALUE : 0.091 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 470 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) : 0.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 0.83 REMARK 3 REFLECTION IN BIN (WORKING SET) : 175 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 22.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.1210 REMARK 3 BIN FREE R VALUE SET COUNT : 12 REMARK 3 BIN FREE R VALUE : 0.1410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 134 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 3.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : 0.06000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.010 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.010 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.006 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.192 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.990 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.988 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 144 ; 0.014 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 128 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 198 ; 2.147 ; 2.021 REMARK 3 BOND ANGLES OTHERS (DEGREES): 303 ; 1.105 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 19 ; 7.534 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 6 ;39.758 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 18 ;12.362 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 1 ;14.941 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 21 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 162 ; 0.012 ; 0.023 REMARK 3 GENERAL PLANES OTHERS (A): 23 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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): 272 ; 1.516 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 8 ;11.269 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 274 ; 3.984 ; 5.000 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.70 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 THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5OQZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200006137. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.799905 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION MARCH 30, 2013 REMARK 200 DATA SCALING SOFTWARE : XPREP V. 2014/2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9545 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 81.8 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.8500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: PRISMATIC REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 15.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.7 M SODIUM ACETATE PH 4.6, 30%(V/V) REMARK 280 GLYCEROL, 4.6%(W/V) PEG 4000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 13.62150 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 9 OE2 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 H2 GLY A 1 CD GLU A 9 1.03 REMARK 500 H1 GLY A 1 CD GLU A 9 1.26 REMARK 500 N GLY A 1 CD GLU A 9 1.33 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 7 51.96 -91.13 REMARK 500 ALA A 13 -51.84 -121.17 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 110 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 111 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A 112 DISTANCE = 7.57 ANGSTROMS DBREF 5OQZ A 1 18 UNP I0HM07 I0HM07_RUBGI 21 38 SEQRES 1 A 18 GLY ALA PRO SER LEU ILE ASN SER GLU ASP ASN PRO ALA SEQRES 2 A 18 PHE PRO GLN ARG VAL FORMUL 2 HOH *12(H2 O) SHEET 1 AA1 2 ALA A 2 PRO A 3 0 SHEET 2 AA1 2 GLN A 16 ARG A 17 -1 O ARG A 17 N ALA A 2 CRYST1 15.034 27.243 15.174 90.00 116.76 90.00 P 1 21 1 2 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 0.066516 0.000000 0.033546 0.00000 SCALE2 0.000000 0.036707 0.000000 0.00000 SCALE3 0.000000 0.000000 0.073809 0.00000