HEADER DE NOVO PROTEIN 06-DEC-16 5U5A TITLE COILED COIL PEPTIDE METAL COORDINATION FRAMEWORK: DIMER FOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGNED DIMERIC COILED COIL PEPTIDE WITH TWO TERPYRIDINE COMPND 3 SIDE CHAINS; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DESIGNED PEPTIDE, SYNTHETIC, METAL COORDINATION FRAMEWORK, KEYWDS 2 SUPRAMOLECULAR ASSEMBLY, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.A.TAVENOR,M.J.MURNIN,W.S.HORNE REVDAT 5 15-NOV-23 5U5A 1 LINK REVDAT 4 04-OCT-23 5U5A 1 LINK REVDAT 3 27-NOV-19 5U5A 1 REMARK REVDAT 2 20-SEP-17 5U5A 1 REMARK REVDAT 1 22-FEB-17 5U5A 0 JRNL AUTH N.A.TAVENOR,M.J.MURNIN,W.S.HORNE JRNL TITL SUPRAMOLECULAR METAL-COORDINATION POLYMERS, NETS, AND JRNL TITL 2 FRAMEWORKS FROM SYNTHETIC COILED-COIL PEPTIDES. JRNL REF J. AM. CHEM. SOC. V. 139 2212 2017 JRNL REFN ESSN 1520-5126 JRNL PMID 28161945 JRNL DOI 10.1021/JACS.7B00651 REMARK 2 REMARK 2 RESOLUTION. 3.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 1400 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.300 REMARK 3 R VALUE (WORKING SET) : 0.299 REMARK 3 FREE R VALUE : 0.313 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 141 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.970 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 : 0.005 273 REMARK 3 ANGLE : 1.288 371 REMARK 3 CHIRALITY : 0.032 36 REMARK 3 PLANARITY : 0.006 42 REMARK 3 DIHEDRAL : 28.890 96 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 0 THROUGH 30 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.4171 -14.1121 -2.4391 REMARK 3 T TENSOR REMARK 3 T11: 1.3679 T22: 1.1924 REMARK 3 T33: 0.6616 T12: -0.2522 REMARK 3 T13: 0.0932 T23: 0.0761 REMARK 3 L TENSOR REMARK 3 L11: 9.8697 L22: 7.1323 REMARK 3 L33: 9.3164 L12: -2.8847 REMARK 3 L13: 2.7255 L23: -1.1187 REMARK 3 S TENSOR REMARK 3 S11: 0.5840 S12: -1.8292 S13: 0.2360 REMARK 3 S21: -0.1561 S22: -0.8653 S23: -0.2957 REMARK 3 S31: 0.6444 S32: 0.5096 S33: 0.3046 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 5U5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1000225332. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1430 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.230 REMARK 200 RESOLUTION RANGE LOW (A) : 31.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.670 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.15 REMARK 200 R MERGE FOR SHELL (I) : 0.29800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4DZM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 77.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS WITH 2 MM TEREPHTHALIC REMARK 280 ACID PH 6.5, 10 MM COPPER(II) CHLORIDE, 10% W/V PEG 4000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 26.72833 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 53.45667 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 40.09250 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 66.82083 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 13.36417 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 26.72833 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 53.45667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 66.82083 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 40.09250 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 13.36417 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 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 0.00000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -13.36417 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 A 201 12545 2.16 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 CU A 101 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 7WJ A 7 NT2 REMARK 620 2 7WJ A 7 NU1 80.0 REMARK 620 3 7WJ A 7 NU3 80.7 160.8 REMARK 620 4 GLU A 14 OE1 82.4 72.0 105.5 REMARK 620 5 HOH A 201 O 74.3 63.4 111.0 11.2 REMARK 620 6 HOH A 201 O 107.0 105.3 80.4 38.6 49.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 102 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 22 OE1 REMARK 620 2 7WJ A 27 NT2 25.5 REMARK 620 3 7WJ A 27 NU1 31.9 8.1 REMARK 620 4 7WJ A 27 NU3 20.8 5.0 12.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5U59 RELATED DB: PDB REMARK 900 RELATED ID: 5U5B RELATED DB: PDB REMARK 900 RELATED ID: 5U5C RELATED DB: PDB DBREF 5U5A A 0 30 PDB 5U5A 5U5A 0 30 SEQRES 1 A 31 ACE GLU ILE ALA ALA LEU LYS 7WJ GLU ASN ALA ALA LEU SEQRES 2 A 31 LYS GLU GLU ILE ALA ALA LEU LYS LYS GLU ILE ALA ALA SEQRES 3 A 31 LEU 7WJ LYS GLY NH2 HET ACE A 0 3 HET 7WJ A 7 27 HET 7WJ A 27 27 HET NH2 A 30 1 HET CU A 101 1 HET CU A 102 1 HETNAM ACE ACETYL GROUP HETNAM 7WJ (2S)-2-AMINO-4-[([1~2~,2~2~:2~6~,3~2~-TERPYRIDINE]- HETNAM 2 7WJ 2~4~-CARBONYL)AMINO]BUTANOIC ACID HETNAM NH2 AMINO GROUP HETNAM CU COPPER (II) ION FORMUL 1 ACE C2 H4 O FORMUL 1 7WJ 2(C20 H19 N5 O3) FORMUL 1 NH2 H2 N FORMUL 2 CU 2(CU 2+) FORMUL 4 HOH *2(H2 O) HELIX 1 AA1 GLU A 1 GLY A 29 1 29 LINK C ACE A 0 N GLU A 1 1555 1555 1.33 LINK C LYS A 6 N 7WJ A 7 1555 1555 1.33 LINK C 7WJ A 7 N GLU A 8 1555 1555 1.33 LINK C LEU A 26 N 7WJ A 27 1555 1555 1.33 LINK C 7WJ A 27 N LYS A 28 1555 1555 1.33 LINK C GLY A 29 N NH2 A 30 1555 1555 1.33 LINK NT2 7WJ A 7 CU CU A 101 1555 1555 1.97 LINK NU1 7WJ A 7 CU CU A 101 1555 1555 2.17 LINK NU3 7WJ A 7 CU CU A 101 1555 1555 2.18 LINK OE1 GLU A 14 CU CU A 101 1555 12545 1.90 LINK OE1 GLU A 22 CU CU A 102 1555 6555 1.90 LINK NT2 7WJ A 27 CU CU A 102 1555 1555 1.98 LINK NU1 7WJ A 27 CU CU A 102 1555 1555 2.17 LINK NU3 7WJ A 27 CU CU A 102 1555 1555 2.18 LINK CU CU A 101 O HOH A 201 1555 1555 2.62 LINK CU CU A 101 O HOH A 201 1555 12545 2.49 SITE 1 AC1 3 7WJ A 7 GLU A 14 HOH A 201 SITE 1 AC2 3 GLU A 22 7WJ A 27 HOH A 202 CRYST1 57.141 57.141 80.185 90.00 90.00 120.00 P 61 2 2 12 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 0.017500 0.010104 0.000000 0.00000 SCALE2 0.000000 0.020208 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012471 0.00000 HETATM 1 C ACE A 0 43.604 -18.829 -1.354 1.00218.69 C ANISOU 1 C ACE A 0 22613 36089 24390 2732 905 7114 C HETATM 2 O ACE A 0 42.631 -18.108 -1.150 1.00213.36 O ANISOU 2 O ACE A 0 22374 34968 23724 1956 827 6677 O HETATM 3 CH3 ACE A 0 44.580 -19.160 -0.225 1.00225.10 C ANISOU 3 CH3 ACE A 0 22637 37743 25150 2818 357 7367 C