HEADER DE NOVO PROTEIN 29-JAN-20 6XY1 TITLE CRYSTAL STRUCTURE OF A DE NOVO DESIGNED PARALLEL FOUR-HELIX COILED TITLE 2 COIL, 4-KE-4. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-KE-4; COMPND 3 CHAIN: A, B, C, D; 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, TETRAMER, PARALLEL, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.L.EDGELL,N.J.SAVERY,D.N.WOOLFSON REVDAT 4 08-MAR-23 6XY1 1 TITLE REVDAT 3 20-APR-22 6XY1 1 COMPND REMARK DBREF LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 25-MAR-20 6XY1 1 JRNL REVDAT 1 18-MAR-20 6XY1 0 JRNL AUTH C.L.EDGELL,N.J.SAVERY,D.N.WOOLFSON JRNL TITL ROBUSTDE NOVO-DESIGNED HOMOTETRAMERIC COILED COILS. JRNL REF BIOCHEMISTRY V. 59 1087 2020 JRNL REFN ISSN 0006-2960 JRNL PMID 32133841 JRNL DOI 10.1021/ACS.BIOCHEM.0C00082 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16-3546 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 22824 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.210 REMARK 3 FREE R VALUE TEST SET COUNT : 961 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 53.5200 - 2.8700 1.00 3207 124 0.1702 0.2079 REMARK 3 2 2.8700 - 2.2800 1.00 3131 130 0.1641 0.1772 REMARK 3 3 2.2800 - 1.9900 1.00 3106 145 0.1461 0.1528 REMARK 3 4 1.9900 - 1.8100 1.00 3143 129 0.1587 0.1882 REMARK 3 5 1.8100 - 1.6800 1.00 3056 166 0.1576 0.1953 REMARK 3 6 1.6800 - 1.5800 1.00 3138 111 0.1528 0.2154 REMARK 3 7 1.5800 - 1.5000 1.00 3082 156 0.1587 0.1910 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) : 0.132 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.967 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.26 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 : 0.006 1065 REMARK 3 ANGLE : 0.735 1404 REMARK 3 CHIRALITY : 0.033 147 REMARK 3 PLANARITY : 0.003 177 REMARK 3 DIHEDRAL : 24.510 468 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 6XY1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292106488. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-18 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.2.2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22852 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 53.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 13.40 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.0 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M SODIUM CITRATE, PH 6.5, REMARK 280 SUPPLEMENTED WITH 25% GLYCEROL FOR CRYO-PROTECTION, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 25.14000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.71000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 12.57000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 31 REMARK 465 NH2 C 31 REMARK 465 NH2 D 31 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 HOH A 103 O HOH A 137 1.83 REMARK 500 O HOH C 126 O HOH C 139 1.91 REMARK 500 O HOH D 123 O HOH D 124 1.99 REMARK 500 O HOH A 124 O HOH A 140 2.07 REMARK 500 NE2 GLN D 11 O HOH D 101 2.07 REMARK 500 O HOH C 101 O HOH C 124 2.08 REMARK 500 OE1 GLN D 11 O HOH D 102 2.12 REMARK 500 OE2 GLU D 23 O HOH D 103 2.14 REMARK 500 NZ LYS A 22 O HOH A 101 2.16 REMARK 500 NE2 GLN C 13 O HOH D 102 2.16 REMARK 500 O HOH C 113 O HOH D 137 2.17 REMARK 500 OE2 GLU C 23 O HOH C 101 2.17 REMARK 500 O HOH C 128 O HOH C 130 2.17 REMARK 500 O HOH A 125 O HOH A 134 2.18 REMARK 500 O HOH A 102 O HOH A 140 2.18 REMARK 500 OE1 GLU A 16 O HOH A 102 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ACE B 0 and GLY B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide NH2 B 101 and GLY B REMARK 800 30 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ACE C 0 and GLY C 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ACE D 0 and GLY D 1 DBREF 6XY1 A 0 31 PDB 6XY1 6XY1 0 31 DBREF 6XY1 B 0 101 PDB 6XY1 6XY1 0 101 DBREF 6XY1 C 0 31 PDB 6XY1 6XY1 0 31 DBREF 6XY1 D 0 31 PDB 6XY1 6XY1 0 31 SEQRES 1 A 32 ACE GLY GLU ILE GLN LYS GLN LEU LYS GLU ILE GLN LYS SEQRES 2 A 32 GLN LEU LYS GLU ILE GLN TRP GLN LEU LYS GLU ILE GLN SEQRES 3 A 32 LYS GLN LEU LYS GLY NH2 SEQRES 1 B 32 ACE GLY GLU ILE GLN LYS GLN LEU LYS GLU ILE GLN LYS SEQRES 2 B 32 GLN LEU LYS GLU ILE GLN TRP GLN LEU LYS GLU ILE GLN SEQRES 3 B 32 LYS GLN LEU LYS GLY NH2 SEQRES 1 C 32 ACE GLY GLU ILE GLN LYS GLN LEU LYS GLU ILE GLN LYS SEQRES 2 C 32 GLN LEU LYS GLU ILE GLN TRP GLN LEU LYS GLU ILE GLN SEQRES 3 C 32 LYS GLN LEU LYS GLY NH2 SEQRES 1 D 32 ACE GLY GLU ILE GLN LYS GLN LEU LYS GLU ILE GLN LYS SEQRES 2 D 32 GLN LEU LYS GLU ILE GLN TRP GLN LEU LYS GLU ILE GLN SEQRES 3 D 32 LYS GLN LEU LYS GLY NH2 HET ACE A 0 3 HET ACE B 0 3 HET NH2 B 101 1 HET ACE C 0 3 HET ACE D 0 3 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 1 ACE 4(C2 H4 O) FORMUL 2 NH2 H2 N FORMUL 5 HOH *160(H2 O) HELIX 1 AA1 GLY A 1 GLY A 30 1 30 HELIX 2 AA2 GLY B 1 LEU B 28 1 28 HELIX 3 AA3 GLU C 2 GLY C 30 1 29 HELIX 4 AA4 GLY D 1 GLY D 30 1 30 LINK C ACE A 0 N GLY A 1 1555 1555 1.33 LINK C ACE B 0 N GLY B 1 1555 1555 1.33 LINK C GLY B 30 N NH2 B 101 1555 1555 1.43 LINK C ACE C 0 N GLY C 1 1555 1555 1.33 LINK C ACE D 0 N GLY D 1 1555 1555 1.33 SITE 1 AC1 5 GLU B 2 ILE B 3 GLN B 4 LYS B 5 SITE 2 AC1 5 LYS B 15 SITE 1 AC2 8 GLN A 6 HOH A 108 LEU B 28 LYS B 29 SITE 2 AC2 8 HOH B 216 HOH B 217 GLN C 11 HOH C 111 SITE 1 AC3 4 GLU C 2 ILE C 3 GLN C 6 GLN D 4 SITE 1 AC4 7 LYS B 26 HOH B 205 GLU D 2 ILE D 3 SITE 2 AC4 7 GLN D 4 LYS D 5 HOH D 122 CRYST1 53.520 53.520 50.280 90.00 90.00 90.00 P 43 16 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 0.018685 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018685 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019889 0.00000 HETATM 1 C ACE A 0 10.375 52.693 -3.825 1.00 9.52 C HETATM 2 O ACE A 0 9.985 53.079 -4.931 1.00 11.23 O HETATM 3 CH3 ACE A 0 9.864 53.253 -2.537 1.00 8.15 C