HEADER DE NOVO PROTEIN 13-JUL-22 7YH8 TITLE CRYSTAL STRUCTURE OF A HETEROCHIRAL PROTEIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-19437; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: D-PEP-1; COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: D AMINO ACID 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 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: ARTIFICIAL SEQUENCES; SOURCE 9 ORGANISM_TAXID: 81077 KEYWDS HETEROCHIRAL, MINIPROTEIN, ALPHA HELIX, D-PROTEIN, D-PEPTIDE, MIRROR- KEYWDS 2 IMAGE, DE NOVO, DESIGNER, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.LIANG,S.LI,T.WANG,L.LIU,P.LU REVDAT 3 13-NOV-24 7YH8 1 REMARK REVDAT 2 25-SEP-24 7YH8 1 JRNL REVDAT 1 19-JUL-23 7YH8 0 JRNL AUTH K.SUN,S.LI,B.ZHENG,Y.ZHU,T.WANG,M.LIANG,Y.YAO,K.ZHANG, JRNL AUTH 2 J.ZHANG,H.LI,D.HAN,J.ZHENG,B.COVENTRY,L.CAO,D.BAKER,L.LIU, JRNL AUTH 3 P.LU JRNL TITL ACCURATE DE NOVO DESIGN OF HETEROCHIRAL PROTEIN-PROTEIN JRNL TITL 2 INTERACTIONS JRNL REF CELL RES. 2024 JRNL REFN ISSN 1001-0602 JRNL DOI 10.1038/S41422-024-01014-2 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.530 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 8351 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 430 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 24.3700 - 3.1700 0.99 2773 148 0.2052 0.2523 REMARK 3 2 3.1700 - 2.5200 1.00 2637 158 0.2170 0.2515 REMARK 3 3 2.5200 - 2.2000 0.95 2511 124 0.1694 0.2361 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.95 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7YH8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300030773. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : AGILENT ATLAS CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 7.8 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 V721.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8507 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000 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) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.17200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 8000, 100MM TRIS REMARK 280 BASE/HYDROCHLORIC ACID PH8.5, 100MM MAGNESIUM CHLORIDE, 20% (V/V) REMARK 280 PEG400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 27.03200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.96100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.03200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.96100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 REMARK 350 BIOMOLECULE: 2 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: 1310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 HOH B 110 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 107 LIES ON A SPECIAL POSITION. DBREF 7YH8 A 1 62 PDB 7YH8 7YH8 1 62 DBREF 7YH8 B 1 19 PDB 7YH8 7YH8 1 19 DBREF 7YH8 C 1 62 PDB 7YH8 7YH8 1 62 DBREF 7YH8 D 1 19 PDB 7YH8 7YH8 1 19 SEQRES 1 A 62 LEU PRO VAL GLU LYS ILE ILE ARG GLU ALA LYS LYS ILE SEQRES 2 A 62 LEU ASP GLU LEU LEU LYS ARG GLY LEU ILE ASP PRO GLU SEQRES 3 A 62 LEU ALA ARG ILE ALA ARG GLU VAL LEU GLU ARG ALA ARG SEQRES 4 A 62 LYS LEU GLY ASN GLU GLU ALA ALA ARG PHE VAL LEU GLU SEQRES 5 A 62 LEU ILE GLU ARG LEU ARG ARG GLU LEU SER SEQRES 1 B 19 DAS DGL DHI DGL DLE DLE DGL DTH DAL DAL DAR DTR DPN SEQRES 2 B 19 DTY DGL DIL DAL DLY DAR SEQRES 1 C 62 LEU PRO VAL GLU LYS ILE ILE ARG GLU ALA LYS LYS ILE SEQRES 2 C 62 LEU ASP GLU LEU LEU LYS ARG GLY LEU ILE ASP PRO GLU SEQRES 3 C 62 LEU ALA ARG ILE ALA ARG GLU VAL LEU GLU ARG ALA ARG SEQRES 4 C 62 LYS LEU GLY ASN GLU GLU ALA ALA ARG PHE VAL LEU GLU SEQRES 5 C 62 LEU ILE GLU ARG LEU ARG ARG GLU LEU SER SEQRES 1 D 19 DAS DGL DHI DGL DLE DLE DGL DTH DAL DAL DAR DTR DPN SEQRES 2 D 19 DTY DGL DIL DAL DLY DAR HET DAS B 1 8 HET DGL B 2 9 HET DHI B 3 10 HET DGL B 4 9 HET DLE B 5 8 HET DLE B 6 8 HET DGL B 7 9 HET DTH B 8 7 HET DAL B 9 5 HET DAL B 10 5 HET DAR B 11 11 HET DTR B 12 14 HET DPN B 13 11 HET DTY B 14 12 HET DGL B 15 9 HET DIL B 16 8 HET DAL B 17 5 HET DLY B 18 9 HET DAR B 19 11 HET DAS D 1 8 HET DGL D 2 9 HET DHI D 3 10 HET DGL D 4 9 HET DLE D 5 8 HET DLE D 6 8 HET DGL D 7 9 HET DTH D 8 7 HET DAL D 9 5 HET DAL D 10 5 HET DAR D 11 11 HET DTR D 12 14 HET DPN D 13 11 HET DTY D 14 12 HET DGL D 15 9 HET DIL D 16 8 HET DAL D 17 5 HET DLY D 18 9 HET DAR D 19 11 HETNAM DAS D-ASPARTIC ACID HETNAM DGL D-GLUTAMIC ACID HETNAM DHI D-HISTIDINE HETNAM DLE D-LEUCINE HETNAM DTH D-THREONINE HETNAM DAL D-ALANINE HETNAM DAR D-ARGININE HETNAM DTR D-TRYPTOPHAN HETNAM DPN D-PHENYLALANINE HETNAM DTY D-TYROSINE HETNAM DIL D-ISOLEUCINE HETNAM DLY D-LYSINE FORMUL 2 DAS 2(C4 H7 N O4) FORMUL 2 DGL 8(C5 H9 N O4) FORMUL 2 DHI 2(C6 H10 N3 O2 1+) FORMUL 2 DLE 4(C6 H13 N O2) FORMUL 2 DTH 2(C4 H9 N O3) FORMUL 2 DAL 6(C3 H7 N O2) FORMUL 2 DAR 4(C6 H15 N4 O2 1+) FORMUL 2 DTR 2(C11 H12 N2 O2) FORMUL 2 DPN 2(C9 H11 N O2) FORMUL 2 DTY 2(C9 H11 N O3) FORMUL 2 DIL 2(C6 H13 N O2) FORMUL 2 DLY 2(C6 H14 N2 O2) FORMUL 5 HOH *80(H2 O) HELIX 1 AA1 LEU A 1 ARG A 20 1 20 HELIX 2 AA2 ASP A 24 GLY A 42 1 19 HELIX 3 AA3 ASN A 43 SER A 62 1 20 HELIX 4 AA4 DGL B 2 DAR B 19 1 18 HELIX 5 AA5 PRO C 2 ARG C 20 1 19 HELIX 6 AA6 ASP C 24 GLY C 42 1 19 HELIX 7 AA7 ASN C 43 SER C 62 1 20 HELIX 8 AA8 DGL D 2 DAR D 19 1 18 LINK C DAS B 1 N DGL B 2 1555 1555 1.33 LINK C DGL B 2 N DHI B 3 1555 1555 1.33 LINK C DHI B 3 N DGL B 4 1555 1555 1.33 LINK C DGL B 4 N DLE B 5 1555 1555 1.33 LINK C DLE B 5 N DLE B 6 1555 1555 1.34 LINK C DLE B 6 N DGL B 7 1555 1555 1.34 LINK C DGL B 7 N DTH B 8 1555 1555 1.33 LINK C DTH B 8 N DAL B 9 1555 1555 1.33 LINK C DAL B 9 N DAL B 10 1555 1555 1.33 LINK C DAL B 10 N DAR B 11 1555 1555 1.34 LINK C DAR B 11 N DTR B 12 1555 1555 1.33 LINK C DTR B 12 N DPN B 13 1555 1555 1.33 LINK C DPN B 13 N DTY B 14 1555 1555 1.34 LINK C DTY B 14 N DGL B 15 1555 1555 1.33 LINK C DGL B 15 N DIL B 16 1555 1555 1.33 LINK C DIL B 16 N DAL B 17 1555 1555 1.34 LINK C DAL B 17 N DLY B 18 1555 1555 1.33 LINK C DLY B 18 N DAR B 19 1555 1555 1.33 LINK C DAS D 1 N DGL D 2 1555 1555 1.33 LINK C DGL D 2 N DHI D 3 1555 1555 1.33 LINK C DHI D 3 N DGL D 4 1555 1555 1.33 LINK C DGL D 4 N DLE D 5 1555 1555 1.33 LINK C DLE D 5 N DLE D 6 1555 1555 1.33 LINK C DLE D 6 N DGL D 7 1555 1555 1.33 LINK C DGL D 7 N DTH D 8 1555 1555 1.33 LINK C DTH D 8 N DAL D 9 1555 1555 1.33 LINK C DAL D 9 N DAL D 10 1555 1555 1.33 LINK C DAL D 10 N DAR D 11 1555 1555 1.33 LINK C DAR D 11 N DTR D 12 1555 1555 1.33 LINK C DTR D 12 N DPN D 13 1555 1555 1.33 LINK C DPN D 13 N DTY D 14 1555 1555 1.33 LINK C DTY D 14 N DGL D 15 1555 1555 1.33 LINK C DGL D 15 N DIL D 16 1555 1555 1.33 LINK C DIL D 16 N DAL D 17 1555 1555 1.33 LINK C DAL D 17 N DLY D 18 1555 1555 1.33 LINK C DLY D 18 N DAR D 19 1555 1555 1.33 CRYST1 54.064 81.922 35.722 90.00 90.00 90.00 P 21 21 2 8 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 0.018497 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012207 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027994 0.00000