HEADER DE NOVO PROTEIN 17-JUN-20 7CCN TITLE THE BINDING STRUCTURE OF A LANTHANIDE BINDING TAG (LBT3) WITH LUTETIUM TITLE 2 ION (LU3+) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LBT3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS LANTHANIDE-BINDING PEPTIDE LANTHANUM ION, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.HATANAKA,N.KIKKAWA,A.MATSUGAMI,Y.HOSOKAWA,F.HAYASHI,N.ISHIDA REVDAT 3 15-MAY-24 7CCN 1 REMARK REVDAT 2 14-JUN-23 7CCN 1 REMARK REVDAT 1 28-APR-21 7CCN 0 JRNL AUTH T.HATANAKA,N.KIKKAWA,A.MATSUGAMI,Y.HOSOKAWA,F.HAYASHI, JRNL AUTH 2 N.ISHIDA JRNL TITL THE ORIGINS OF BINDING SPECIFICITY OF A LANTHANIDE ION JRNL TITL 2 BINDING PEPTIDE. JRNL REF SCI REP V. 10 19468 2020 JRNL REFN ESSN 2045-2322 JRNL PMID 33173124 JRNL DOI 10.1038/S41598-020-76527-Y REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMACS REMARK 3 AUTHORS : JUSTIN A. LEMKUL, REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7CCN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1300017357. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 30-100 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 500 UM LBT3, 30 MM [U-99% 2H] REMARK 210 MES, 1000 UM LUTETIUM (III) ION, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, SPARKY 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 : TARGET FUNCTION 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: 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 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 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -9.6 DEGREES REMARK 500 1 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -9.0 DEGREES REMARK 500 2 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -9.4 DEGREES REMARK 500 2 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -8.7 DEGREES REMARK 500 3 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -9.3 DEGREES REMARK 500 3 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -8.9 DEGREES REMARK 500 4 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -9.5 DEGREES REMARK 500 4 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -8.6 DEGREES REMARK 500 5 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -9.6 DEGREES REMARK 500 5 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -8.8 DEGREES REMARK 500 6 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -9.0 DEGREES REMARK 500 6 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -8.6 DEGREES REMARK 500 7 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -9.5 DEGREES REMARK 500 7 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -8.0 DEGREES REMARK 500 8 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -8.8 DEGREES REMARK 500 8 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -8.0 DEGREES REMARK 500 9 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -8.9 DEGREES REMARK 500 9 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -8.8 DEGREES REMARK 500 10 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -8.8 DEGREES REMARK 500 10 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -7.6 DEGREES REMARK 500 11 ASP A 7 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 11 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -9.6 DEGREES REMARK 500 11 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -8.0 DEGREES REMARK 500 12 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -9.7 DEGREES REMARK 500 13 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -9.0 DEGREES REMARK 500 13 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -9.1 DEGREES REMARK 500 14 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -9.1 DEGREES REMARK 500 14 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -7.9 DEGREES REMARK 500 15 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -9.6 DEGREES REMARK 500 15 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -8.2 DEGREES REMARK 500 16 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -9.2 DEGREES REMARK 500 16 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -8.8 DEGREES REMARK 500 17 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -8.9 DEGREES REMARK 500 17 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -8.2 DEGREES REMARK 500 18 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -8.8 DEGREES REMARK 500 18 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -9.7 DEGREES REMARK 500 19 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -9.4 DEGREES REMARK 500 19 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -9.3 DEGREES REMARK 500 20 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -9.2 DEGREES REMARK 500 20 GLU A 14 OE1 - CD - OE2 ANGL. DEV. = -8.5 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 ASN A 6 63.32 35.94 REMARK 500 14 ASN A 6 40.38 71.97 REMARK 500 18 ASN A 6 70.16 47.20 REMARK 500 19 ASN A 6 64.59 33.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 LU A 101 LU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 3 OD1 REMARK 620 2 ASN A 5 OD1 82.0 REMARK 620 3 ASP A 7 OD1 76.1 81.3 REMARK 620 4 ASP A 7 OD2 120.7 71.6 48.5 REMARK 620 5 TRP A 9 O 78.8 151.8 74.2 100.9 REMARK 620 6 GLU A 11 OE1 149.8 126.5 96.7 68.1 71.0 REMARK 620 7 GLU A 11 OE2 150.5 79.1 122.5 74.0 126.1 57.0 REMARK 620 8 GLU A 14 OE1 75.8 70.5 142.4 135.5 123.4 119.9 76.7 REMARK 620 9 GLU A 14 OE2 87.7 126.1 146.2 150.1 73.7 82.5 85.4 55.7 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LU A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36356 RELATED DB: BMRB REMARK 900 THE BINDING STRUCTURE OF A LANTHANIDE BINDING TAG (LBT3) WITH REMARK 900 LUTETIUM ION (LU3+) DBREF 7CCN A 1 17 PDB 7CCN 7CCN 1 17 SEQRES 1 A 17 PHE ILE ASP THR ASN ASN ASP GLY TRP ILE GLU GLY ASP SEQRES 2 A 17 GLU LEU LEU ALA HET LU A 101 1 HETNAM LU LUTETIUM (III) ION HETSYN LU LU FORMUL 2 LU LU 3+ HELIX 1 AA1 GLU A 11 ALA A 17 5 7 LINK OD1 ASP A 3 LU LU A 101 1555 1555 2.16 LINK OD1 ASN A 5 LU LU A 101 1555 1555 2.32 LINK OD1 ASP A 7 LU LU A 101 1555 1555 2.17 LINK OD2 ASP A 7 LU LU A 101 1555 1555 2.81 LINK O TRP A 9 LU LU A 101 1555 1555 2.39 LINK OE1 GLU A 11 LU LU A 101 1555 1555 2.20 LINK OE2 GLU A 11 LU LU A 101 1555 1555 2.20 LINK OE1 GLU A 14 LU LU A 101 1555 1555 2.31 LINK OE2 GLU A 14 LU LU A 101 1555 1555 2.20 SITE 1 AC1 6 ASP A 3 ASN A 5 ASP A 7 TRP A 9 SITE 2 AC1 6 GLU A 11 GLU A 14 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 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.503 3.134 1.764 1.00 0.00 LU ENDMDL MODEL 2 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.476 3.085 1.821 1.00 0.00 LU ENDMDL MODEL 3 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.464 3.199 1.949 1.00 0.00 LU ENDMDL MODEL 4 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.438 3.209 1.868 1.00 0.00 LU ENDMDL MODEL 5 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.460 3.115 1.861 1.00 0.00 LU ENDMDL MODEL 6 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.646 3.137 1.868 1.00 0.00 LU ENDMDL MODEL 7 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.442 3.144 1.850 1.00 0.00 LU ENDMDL MODEL 8 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.473 3.170 1.943 1.00 0.00 LU ENDMDL MODEL 9 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.509 3.112 1.903 1.00 0.00 LU ENDMDL MODEL 10 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.427 3.202 1.959 1.00 0.00 LU ENDMDL MODEL 11 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.494 3.180 1.887 1.00 0.00 LU ENDMDL MODEL 12 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.495 3.198 1.955 1.00 0.00 LU ENDMDL MODEL 13 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.461 3.200 2.008 1.00 0.00 LU ENDMDL MODEL 14 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.504 3.199 1.846 1.00 0.00 LU ENDMDL MODEL 15 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.387 3.180 2.008 1.00 0.00 LU ENDMDL MODEL 16 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.418 3.118 1.813 1.00 0.00 LU ENDMDL MODEL 17 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.507 3.161 1.859 1.00 0.00 LU ENDMDL MODEL 18 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.449 3.312 1.814 1.00 0.00 LU ENDMDL MODEL 19 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.381 3.125 1.810 1.00 0.00 LU ENDMDL MODEL 20 TER 253 ALA A 17 HETATM 254 LU LU A 101 1.340 3.123 1.859 1.00 0.00 LU ENDMDL CONECT 46 254 CONECT 72 254 CONECT 100 254 CONECT 101 254 CONECT 116 254 CONECT 163 254 CONECT 164 254 CONECT 197 254 CONECT 198 254 CONECT 254 46 72 100 101 CONECT 254 116 163 164 197 CONECT 254 198 MASTER 173 0 1 1 0 0 2 6 136 1 12 2 END