HEADER DE NOVO PROTEIN 31-MAY-18 6DLC TITLE DESIGNED PROTEIN DHD1:234_A, DESIGNED PROTEIN DHD1:234_B COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGNED PROTEIN DHD1:234_A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DESIGNED PROTEIN DHD1:234_B; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPUTATIONAL DESIGN, HETERODIMER, COILED-COIL, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.J.BICK,Z.CHEN,D.BAKER REVDAT 6 03-APR-24 6DLC 1 REMARK REVDAT 5 13-MAR-24 6DLC 1 REMARK REVDAT 4 20-NOV-19 6DLC 1 REMARK REVDAT 3 16-JAN-19 6DLC 1 JRNL REVDAT 2 09-JAN-19 6DLC 1 JRNL REVDAT 1 26-DEC-18 6DLC 0 JRNL AUTH Z.CHEN,S.E.BOYKEN,M.JIA,F.BUSCH,D.FLORES-SOLIS,M.J.BICK, JRNL AUTH 2 P.LU,Z.L.VANAERNUM,A.SAHASRABUDDHE,R.A.LANGAN,S.BERMEO, JRNL AUTH 3 T.J.BRUNETTE,V.K.MULLIGAN,L.P.CARTER,F.DIMAIO,N.G.SGOURAKIS, JRNL AUTH 4 V.H.WYSOCKI,D.BAKER JRNL TITL PROGRAMMABLE DESIGN OF ORTHOGONAL PROTEIN HETERODIMERS. JRNL REF NATURE V. 565 106 2019 JRNL REFN ESSN 1476-4687 JRNL PMID 30568301 JRNL DOI 10.1038/S41586-018-0802-Y REMARK 2 REMARK 2 RESOLUTION. 3.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3112 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) : 3.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 2482 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.261 REMARK 3 R VALUE (WORKING SET) : 0.258 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.150 REMARK 3 FREE R VALUE TEST SET COUNT : 252 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 48.4478 - 4.1080 1.00 1125 134 0.2443 0.2699 REMARK 3 2 4.1080 - 3.2609 1.00 1105 118 0.2996 0.3422 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) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 109.0 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 117.0 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 : 0.003 941 REMARK 3 ANGLE : 0.638 1286 REMARK 3 CHIRALITY : 0.034 169 REMARK 3 PLANARITY : 0.005 164 REMARK 3 DIHEDRAL : 8.952 575 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 6DLC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234847. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999954 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL SI(111) AND REMARK 200 MULTILAYER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JUNE 17, 2015 REMARK 200 DATA SCALING SOFTWARE : XDS JUNE 17, 2015 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2485 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.260 REMARK 200 RESOLUTION RANGE LOW (A) : 48.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.12500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 1.34300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6. REMARK 200 STARTING MODEL: COMPUTATIONAL DESIGN MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15M POTASSIUM BROMIDE, 30% (W/V) PEG REMARK 280 2,000 MME, PLUS 20% GLYCEROL AS CRYOPROTECTANT, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 290.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 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 REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 9.28200 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 18.56400 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 9.28200 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 18.56400 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: 5670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 96.88500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MET A 0 REMARK 465 ASP A 1 REMARK 465 SER A 2 REMARK 465 ASP A 3 REMARK 465 GLU A 4 REMARK 465 HIS A 5 REMARK 465 ILE A 76 REMARK 465 ASP A 77 REMARK 465 LYS A 78 REMARK 465 ARG A 79 REMARK 465 HIS B 114 REMARK 465 VAL B 148 REMARK 465 GLU B 149 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 LEU A 6 CG CD1 CD2 REMARK 470 LYS A 8 CG CD CE NZ REMARK 470 LEU A 9 CD1 CD2 REMARK 470 LYS A 10 CG CD CE NZ REMARK 470 LEU A 13 CD1 CD2 REMARK 470 GLU A 14 CG CD OE1 OE2 REMARK 470 LEU A 16 CD1 CD2 REMARK 470 LEU A 20 CD1 CD2 REMARK 470 ASP A 21 CG OD1 OD2 REMARK 470 LYS A 25 CG CD CE NZ REMARK 470 LYS A 28 CD CE NZ REMARK 470 ARG A 31 CD NE CZ NH1 NH2 REMARK 470 ASP A 32 CG OD1 OD2 REMARK 470 ILE A 33 CG1 CG2 CD1 REMARK 470 LEU A 34 CG CD1 CD2 REMARK 470 SER A 35 OG REMARK 470 GLU A 36 CD OE1 OE2 REMARK 470 GLU A 39 CG CD OE1 OE2 REMARK 470 GLU A 41 CG CD OE1 OE2 REMARK 470 LYS A 44 CG CD CE NZ REMARK 470 ILE A 47 CG1 CG2 CD1 REMARK 470 ASP A 48 CG OD1 OD2 REMARK 470 LEU A 49 CD1 CD2 REMARK 470 GLU A 51 CG CD OE1 OE2 REMARK 470 VAL A 54 CG1 CG2 REMARK 470 ARG A 55 CD NE CZ NH1 NH2 REMARK 470 LYS A 58 CG CD CE NZ REMARK 470 ILE A 61 CG1 CG2 CD1 REMARK 470 LYS A 62 CG CD CE NZ REMARK 470 ILE A 63 CG1 CG2 CD1 REMARK 470 GLU A 65 CG CD OE1 OE2 REMARK 470 SER A 67 OG REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 LYS A 71 CD CE NZ REMARK 470 GLU A 72 CG CD OE1 OE2 REMARK 470 LYS A 73 CG CD CE NZ REMARK 470 ARG A 74 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 80 CG OD1 OD2 REMARK 470 LYS A 82 CG CD CE NZ REMARK 470 GLU A 83 CD OE1 OE2 REMARK 470 LEU A 84 CG CD1 CD2 REMARK 470 ASP A 85 OD1 OD2 REMARK 470 LYS A 86 CD CE NZ REMARK 470 LEU A 87 CG CD1 CD2 REMARK 470 LEU A 88 CG CD1 CD2 REMARK 470 ASP A 89 OD1 OD2 REMARK 470 GLU A 92 CG CD OE1 OE2 REMARK 470 LYS A 93 CG CD CE NZ REMARK 470 GLN A 96 CD OE1 NE2 REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 ASP A 104 OD1 OD2 REMARK 470 ASN A 106 OD1 ND2 REMARK 470 LYS A 107 CE NZ REMARK 470 GLU A 110 CD OE1 OE2 REMARK 470 ARG A 113 CD NE CZ NH1 NH2 REMARK 470 ARG A 114 NE CZ NH1 NH2 REMARK 470 LYS B 118 CD CE NZ REMARK 470 GLU B 121 CD OE1 OE2 REMARK 470 GLU B 125 CD OE1 OE2 REMARK 470 LYS B 128 CD CE NZ REMARK 470 ARG B 129 CD NE CZ NH1 NH2 REMARK 470 GLU B 131 CD OE1 OE2 REMARK 470 LYS B 132 CD CE NZ REMARK 470 LYS B 135 CG CD CE NZ REMARK 470 GLU B 136 CD OE1 OE2 REMARK 470 GLU B 139 CD OE1 OE2 REMARK 470 LYS B 142 CD CE NZ REMARK 470 LYS B 146 CG CD CE NZ REMARK 470 LYS B 147 CG CD CE NZ 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 OD1 ASP A 66 NH2 ARG A 69 2.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 6DLC A 0 114 PDB 6DLC 6DLC 0 114 DBREF 6DLC B 114 149 PDB 6DLC 6DLC 114 149 SEQRES 1 A 115 MET ASP SER ASP GLU HIS LEU TYR LYS LEU LYS THR PHE SEQRES 2 A 115 LEU GLU ASN LEU ARG ARG HIS LEU ASP ARG LEU ASP LYS SEQRES 3 A 115 HIS ILE LYS GLN LEU ARG ASP ILE LEU SER GLU ASN PRO SEQRES 4 A 115 GLU ASP GLU ARG VAL LYS ASP ALA ILE ASP LEU SER GLU SEQRES 5 A 115 ARG SER VAL ARG ILE VAL LYS THR VAL ILE LYS ILE PHE SEQRES 6 A 115 GLU ASP SER VAL ARG LYS LYS GLU LYS ARG PRO ILE ASP SEQRES 7 A 115 LYS ARG ASP ASP LYS GLU LEU ASP LYS LEU LEU ASP THR SEQRES 8 A 115 LEU GLU LYS ILE LEU GLN THR ALA THR LYS ILE ILE ASP SEQRES 9 A 115 ASP ALA ASN LYS LEU LEU GLU TYR LEU ARG ARG SEQRES 1 B 36 HIS GLY ASP PRO LYS VAL VAL GLU THR TYR VAL GLU LEU SEQRES 2 B 36 LEU LYS ARG HIS GLU LYS ALA VAL LYS GLU LEU LEU GLU SEQRES 3 B 36 ILE ALA LYS THR HIS ALA LYS LYS VAL GLU HELIX 1 AA1 LEU A 6 ASN A 37 1 32 HELIX 2 AA2 ASP A 40 LYS A 73 1 34 HELIX 3 AA3 ASP A 81 ARG A 114 1 34 HELIX 4 AA4 ASP B 116 LYS B 147 1 32 CRYST1 96.885 96.885 27.846 90.00 90.00 120.00 P 64 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 0.010322 0.005959 0.000000 0.00000 SCALE2 0.000000 0.011918 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035912 0.00000