HEADER DE NOVO PROTEIN 03-FEB-21 7LL7 TITLE [2]CATENANE FROM MCCJ25 VARIANT G12C G21C COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLY-GLY-ALA-GLY-HIS-VAL-PRO-GLU-TYR-PHE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: VAL-CYS-ILE-GLY-THR-PRO-ILE-SER-PHE-TYR-CYS; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 8 ORGANISM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MECHANICALLY INTERLOCKED MOLECULE, LASSO PEPTIDE, CATENANE, DE NOVO KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.J.LINK,H.V.SCHROEDER REVDAT 4 14-JUN-23 7LL7 1 REMARK REVDAT 3 22-SEP-21 7LL7 1 JRNL REVDAT 2 08-SEP-21 7LL7 1 JRNL REVDAT 1 04-AUG-21 7LL7 0 JRNL AUTH H.V.SCHRODER,Y.ZHANG,A.J.LINK JRNL TITL DYNAMIC COVALENT SELF-ASSEMBLY OF MECHANICALLY INTERLOCKED JRNL TITL 2 MOLECULES SOLELY MADE FROM PEPTIDES. JRNL REF NAT.CHEM. V. 13 850 2021 JRNL REFN ESSN 1755-4349 JRNL PMID 34426684 JRNL DOI 10.1038/S41557-021-00770-7 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NAMD 2.13 REMARK 3 AUTHORS : JAMES C. PHILLIPS, DAVID J. HARDY, JULIO D. C. REMARK 3 MAIA, JOHN E. STONE, JOAO V. RIBEIRO, RAFAEL C. REMARK 3 BERNARDI, RONAK BUCH, GIACOMO FIORIN, JEROME HENIN, REMARK 3 WEI JIANG, RYAN MCGREEVY, MARCELO C. R. MELO, REMARK 3 BRIAN K. RADAK, ROBERT D. SKEEL, ABHISHEK REMARK 3 SINGHAROY, YI WANG, BENOIT ROUX, ALEKSEI REMARK 3 AKSIMENTIEV, ZAIDA LUTHEY-SCHULTEN, LAXMIKANT V. REMARK 3 KALE, KLAUS SCHULTEN, CHRISTOPHE CHIPOT, AND EMAD REMARK 3 TAJKHORSHID REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7LL7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1000254577. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 1.03 MM [2]CATENANE, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 1D 1H; 2D 1H-1H REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MESTRELAB (MNOVA / MESTRENOVA / REMARK 210 MESTREC) 14.1.0., CYANA 2.1 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 GLU A 8 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 N GLY A 1 CD GLU A 8 1.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 3 GLU A 8 CD GLU A 8 OE1 -0.083 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 TYR A 9 CB - CG - CD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 TYR A 9 CB - CG - CD1 ANGL. DEV. = -4.8 DEGREES REMARK 500 3 TYR A 9 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 11 TYR A 9 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 11 PHE B 19 CB - CG - CD2 ANGL. DEV. = -5.1 DEGREES REMARK 500 11 PHE B 19 CB - CG - CD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 11 TYR B 20 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 13 PHE A 10 CB - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 14 TYR A 9 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 14 TYR B 20 CB - CG - CD1 ANGL. DEV. = -4.6 DEGREES 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 1 ALA A 3 5.98 -166.66 REMARK 500 1 VAL A 6 108.46 81.13 REMARK 500 2 HIS A 5 -9.24 -150.25 REMARK 500 2 CYS B 12 5.36 -166.89 REMARK 500 3 TYR A 9 41.27 -166.12 REMARK 500 4 ALA A 3 12.38 -161.65 REMARK 500 4 VAL A 6 118.29 74.12 REMARK 500 4 SER B 18 -164.40 -177.69 REMARK 500 5 HIS A 5 -13.32 -142.71 REMARK 500 5 CYS B 12 126.16 176.43 REMARK 500 5 SER B 18 -109.96 -83.23 REMARK 500 6 ALA A 3 -90.48 -132.68 REMARK 500 6 VAL A 6 122.04 75.52 REMARK 500 6 SER B 18 -144.71 -173.90 REMARK 500 8 ALA A 3 -84.00 -140.13 REMARK 500 8 VAL A 6 121.79 70.41 REMARK 500 9 HIS A 5 -21.82 -142.31 REMARK 500 9 TYR A 9 -1.63 -163.89 REMARK 500 10 PRO B 16 150.04 -49.24 REMARK 500 11 HIS A 5 -51.94 -171.31 REMARK 500 12 THR B 15 -57.65 -173.01 REMARK 500 13 HIS A 5 1.92 -150.95 REMARK 500 13 TYR A 9 59.07 -102.59 REMARK 500 13 SER B 18 -88.38 -93.24 REMARK 500 14 HIS A 5 -14.82 -140.48 REMARK 500 15 SER B 18 -159.37 -112.51 REMARK 500 16 SER B 18 -142.47 -87.15 REMARK 500 18 SER B 18 -145.70 173.76 REMARK 500 19 TYR A 9 -91.68 -111.26 REMARK 500 20 HIS A 5 4.89 -155.04 REMARK 500 20 SER B 18 -151.60 -136.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR B 15 PRO B 16 5 -142.64 REMARK 500 THR B 15 PRO B 16 7 -147.20 REMARK 500 THR B 15 PRO B 16 10 138.24 REMARK 500 GLU A 8 TYR A 9 11 149.79 REMARK 500 VAL B 11 CYS B 12 11 139.95 REMARK 500 THR B 15 PRO B 16 14 -144.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 5 TYR B 20 0.07 SIDE CHAIN REMARK 500 7 TYR B 20 0.09 SIDE CHAIN REMARK 500 11 TYR A 9 0.12 SIDE CHAIN REMARK 500 11 TYR B 20 0.06 SIDE CHAIN REMARK 500 15 TYR B 20 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30852 RELATED DB: BMRB REMARK 900 [2]CATENANE FROM MCCJ25 VARIANT G12C G21C DBREF 7LL7 A 1 10 PDB 7LL7 7LL7 1 10 DBREF 7LL7 B 11 21 PDB 7LL7 7LL7 11 21 SEQRES 1 A 10 GLY GLY ALA GLY HIS VAL PRO GLU TYR PHE SEQRES 1 B 11 VAL CYS ILE GLY THR PRO ILE SER PHE TYR CYS SSBOND 1 CYS B 12 CYS B 21 1555 1555 2.05 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1