HEADER DE NOVO PROTEIN 15-SEP-25 9SOM TITLE CRYSTAL STRUCTURE OF A DESIGNED COILED COIL WITH TWO DISTINCT TERBIUM TITLE 2 SITES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGNED COILED COIL WITH TWO DISTINCT TERBIUM SITES; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS COILED COIL, METAL BINDING, TERBIUM, DE NOVO, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.G.CAULTON,A.F.A.PEACOCK,A.L.LOVERING,G.ROSE REVDAT 1 10-JUN-26 9SOM 0 JRNL AUTH L.N.SLOPE,A.SHAH,M.J.TAYLOR,V.BORGHESANI,S.G.CAULTON, JRNL AUTH 2 N.J.BROOKS,K.A.HADLEY,G.ROSE,R.I.HUNTER,H.E.L.MKAMI, JRNL AUTH 3 G.M.SMITH,A.C.LENEY,N.J.BUURMA,A.L.LOVERING,J.E.LOVETT, JRNL AUTH 4 A.F.A.PEACOCK JRNL TITL DESIGN OF A SITE SELECTIVE HETEROCHROMIC BIMETALLIC JRNL TITL 2 LANTHANIDE COILED COIL WITH NANOMETRE-SCALE CONTROL. JRNL REF CHEM SCI 2026 JRNL REFN ISSN 2041-6520 JRNL PMID 42164438 JRNL DOI 10.1039/D6SC00813E REMARK 2 REMARK 2 RESOLUTION. 2.76 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) : 2.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 1466 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 74 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 23.7900 - 2.7600 0.97 1392 74 0.2210 0.2475 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.003 361 REMARK 3 ANGLE : 0.358 479 REMARK 3 CHIRALITY : 0.032 52 REMARK 3 PLANARITY : 0.002 62 REMARK 3 DIHEDRAL : 18.260 146 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3 THROUGH 45 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.2619 10.1586 20.8677 REMARK 3 T TENSOR REMARK 3 T11: 0.6529 T22: 0.9963 REMARK 3 T33: 0.9508 T12: -0.0172 REMARK 3 T13: 0.1189 T23: 0.1494 REMARK 3 L TENSOR REMARK 3 L11: 0.6975 L22: 6.8055 REMARK 3 L33: 2.0021 L12: -1.5385 REMARK 3 L13: -1.9237 L23: 9.1643 REMARK 3 S TENSOR REMARK 3 S11: -1.1029 S12: -0.9620 S13: -0.0541 REMARK 3 S21: 1.7991 S22: 0.2597 S23: 0.4924 REMARK 3 S31: 3.8656 S32: -0.7988 S33: 1.6725 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 9SOM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1292149442. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.4 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 8.0.016 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1507 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.760 REMARK 200 RESOLUTION RANGE LOW (A) : 23.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 20.30 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.99 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 20.50 REMARK 200 R MERGE FOR SHELL (I) : 0.45000 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.0 30 % V/V JEFFAMINE REMARK 280 ED-2003, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 38.74500 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 19.37250 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 33.55415 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 TB TB A 101 LIES ON A SPECIAL POSITION. REMARK 375 TB TB A 102 LIES ON A SPECIAL POSITION. REMARK 375 TB TB A 104 LIES ON A SPECIAL POSITION. 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 TRP A 2 -64.16 62.02 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 TB A 103 TB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 1 OE1 REMARK 620 2 GLU A 1 OE2 54.3 REMARK 620 3 GLU A 3 OE1 16.9 37.9 REMARK 620 4 GLU A 3 OE2 24.8 31.3 8.2 REMARK 620 5 GLU A 6 OE1 25.9 56.2 26.3 27.6 REMARK 620 6 GLU A 6 OE2 30.5 60.2 31.6 32.5 5.4 REMARK 620 7 GLY A 45 O 100.8 77.1 90.7 83.9 76.4 73.2 REMARK 620 8 GLY A 45 OXT 99.8 75.8 89.5 82.7 75.5 72.4 1.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 TB A 104 TB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 12 OD1 REMARK 620 2 ASN A 12 OD1 0.0 REMARK 620 3 ASP A 16 OD1 78.9 78.9 REMARK 620 4 ASP A 16 OD2 83.8 83.8 50.0 REMARK 620 5 ASP A 16 OD1 78.9 78.9 0.0 50.0 REMARK 620 6 ASP A 16 OD2 83.8 83.8 50.0 0.0 50.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 TB A 102 TB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 23 OD1 REMARK 620 2 ASP A 23 OD2 55.8 REMARK 620 3 ASP A 23 OD1 0.0 55.8 REMARK 620 4 ASP A 23 OD2 55.8 0.0 55.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 TB A 101 TB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 38 OE1 REMARK 620 2 GLU A 38 OE2 54.1 REMARK 620 3 GLU A 41 OE1 83.4 111.1 REMARK 620 N 1 2 DBREF 9SOM A 1 45 PDB 9SOM 9SOM 1 45 SEQRES 1 A 45 GLU TRP GLU ALA ILE GLU LYS LYS ILE ALA ALA ASN GLU SEQRES 2 A 45 SER LYS ASP GLN ALA ILE GLU LYS LYS ASP GLN ALA ILE SEQRES 3 A 45 GLU LYS LYS ILE GLN ALA ILE GLU LYS LYS ILE GLU ALA SEQRES 4 A 45 ILE GLU HIS GLY ILE GLY HET TB A 101 1 HET TB A 102 1 HET TB A 103 1 HET TB A 104 1 HETNAM TB TERBIUM(III) ION FORMUL 2 TB 4(TB 3+) FORMUL 6 HOH *(H2 O) HELIX 1 AA1 TRP A 2 ILE A 44 1 43 LINK OE1 GLU A 1 TB TB A 103 1555 6655 2.45 LINK OE2 GLU A 1 TB TB A 103 1555 6655 2.38 LINK OE1 GLU A 3 TB TB A 103 1555 1555 2.79 LINK OE2 GLU A 3 TB TB A 103 1555 1555 2.21 LINK OE1 GLU A 6 TB TB A 103 1555 4665 2.76 LINK OE2 GLU A 6 TB TB A 103 1555 4665 2.60 LINK OD1 ASN A 12 TB TB A 104 1555 1555 2.61 LINK OD1 ASN A 12 TB TB A 104 1555 2655 2.61 LINK OD1 ASP A 16 TB TB A 104 1555 1555 2.75 LINK OD2 ASP A 16 TB TB A 104 1555 1555 2.38 LINK OD1 ASP A 16 TB TB A 104 1555 2655 2.75 LINK OD2 ASP A 16 TB TB A 104 1555 2655 2.38 LINK OD1 ASP A 23 TB TB A 102 1555 1555 2.45 LINK OD2 ASP A 23 TB TB A 102 1555 1555 2.22 LINK OD1 ASP A 23 TB TB A 102 1555 2655 2.45 LINK OD2 ASP A 23 TB TB A 102 1555 2655 2.22 LINK OE1 GLU A 38 TB TB A 101 1555 6555 2.45 LINK OE2 GLU A 38 TB TB A 101 1555 6555 2.38 LINK OE1 GLU A 41 TB TB A 101 1555 6555 2.60 LINK O GLY A 45 TB TB A 103 1555 5554 2.87 LINK OXT GLY A 45 TB TB A 103 1555 5554 2.69 CRYST1 38.745 38.745 67.460 90.00 90.00 120.00 P 6 6 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 0.025810 0.014901 0.000000 0.00000 SCALE2 0.000000 0.029803 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014824 0.00000 CONECT 31 363 CONECT 32 363 CONECT 97 364 CONECT 129 364 CONECT 130 364 CONECT 186 362 CONECT 187 362 CONECT 362 186 187 CONECT 363 31 32 CONECT 364 97 129 130 MASTER 294 0 4 1 0 0 0 6 364 1 10 4 END