HEADER DE NOVO PROTEIN 06-DEC-16 5U59 TITLE COILED COIL PEPTIDE METAL COORDINATION FRAMEWORK: DIMER FOLD GROWN TITLE 2 WITH CITRATE 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 5U59 1 LINK REVDAT 4 04-OCT-23 5U59 1 REMARK REVDAT 3 27-NOV-19 5U59 1 REMARK REVDAT 2 20-SEP-17 5U59 1 REMARK REVDAT 1 22-FEB-17 5U59 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. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.540 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 2374 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 238 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 26.0868 - 2.7715 0.99 1080 119 0.2055 0.2340 REMARK 3 2 2.7715 - 2.2002 0.99 1056 119 0.2905 0.3370 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.850 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 : 0.003 293 REMARK 3 ANGLE : 1.068 400 REMARK 3 CHIRALITY : 0.028 36 REMARK 3 PLANARITY : 0.002 47 REMARK 3 DIHEDRAL : 30.930 105 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5U59 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_1000225331. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2391 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 29.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.42 REMARK 200 R MERGE FOR SHELL (I) : 0.21200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 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 (%): 63.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE PH 6.0, 15% W/V REMARK 280 PEG 4000, 3 MM COPPER(II) CHLORIDE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 18.16300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.08500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 18.16300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.08500 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 -1.000000 0.000000 0.000000 -12.35988 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 49.64659 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 NH2 A 30 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 GLY A 29 CA C O 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 O LEU A 5 ND2 ASN A 9 2.14 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 78.6 REMARK 620 3 7WJ A 7 NU3 79.0 157.6 REMARK 620 4 CIT A 103 O3 165.2 103.4 98.4 REMARK 620 N 1 2 3 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 7WJ A 27 NT2 REMARK 620 2 7WJ A 27 NU1 78.7 REMARK 620 3 7WJ A 27 NU3 78.9 157.6 REMARK 620 4 CIT A 104 O2 157.8 102.6 98.2 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 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 104 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5U5A RELATED DB: PDB REMARK 900 RELATED ID: 5U5B RELATED DB: PDB REMARK 900 RELATED ID: 5U5C RELATED DB: PDB DBREF 5U59 A 0 30 PDB 5U59 5U59 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 CU A 101 1 HET CU A 102 1 HET CIT A 103 13 HET CIT A 104 13 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 CU COPPER (II) ION HETNAM CIT CITRIC ACID FORMUL 1 ACE C2 H4 O FORMUL 1 7WJ 2(C20 H19 N5 O3) FORMUL 2 CU 2(CU 2+) FORMUL 4 CIT 2(C6 H8 O7) FORMUL 6 HOH *27(H2 O) HELIX 1 AA1 GLU A 1 LYS A 28 1 28 LINK C ACE A 0 N GLU A 1 1555 1555 1.34 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 NT2 7WJ A 7 CU CU A 101 1555 1555 1.98 LINK NU1 7WJ A 7 CU CU A 101 1555 1555 2.19 LINK NU3 7WJ A 7 CU CU A 101 1555 1555 2.19 LINK NT2 7WJ A 27 CU CU A 102 1555 1555 1.98 LINK NU1 7WJ A 27 CU CU A 102 1555 1555 2.19 LINK NU3 7WJ A 27 CU CU A 102 1555 1555 2.19 LINK CU CU A 101 O3 CIT A 103 1555 1555 1.82 LINK CU CU A 102 O2 CIT A 104 1555 1555 1.84 SITE 1 AC1 2 7WJ A 7 CIT A 103 SITE 1 AC2 3 7WJ A 27 CIT A 104 HOH A 215 SITE 1 AC3 4 7WJ A 7 7WJ A 27 LYS A 28 CU A 101 SITE 1 AC4 5 LYS A 6 7WJ A 7 7WJ A 27 CU A 102 SITE 2 AC4 5 HOH A 205 CRYST1 36.326 52.170 25.581 90.00 103.98 90.00 C 1 2 1 4 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 0.027528 0.000000 0.006852 0.00000 SCALE2 0.000000 0.019168 0.000000 0.00000 SCALE3 0.000000 0.000000 0.040284 0.00000 HETATM 1 C ACE A 0 0.050 -27.181 22.944 1.00 59.48 C HETATM 2 O ACE A 0 0.398 -26.033 23.226 1.00 43.93 O HETATM 3 CH3 ACE A 0 0.923 -28.372 23.323 1.00 51.70 C