HEADER DE NOVO PROTEIN 12-NOV-20 7DGY TITLE DE NOVO DESIGNED PROTEIN H4C2R COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED PROTEIN H4C2R; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 3 ORGANISM_TAXID: 866768; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS DESIGNED PROTEIN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.XU,S.LIAO,Q.CHEN,H.LIU REVDAT 4 02-MAR-22 7DGY 1 JRNL REVDAT 3 23-FEB-22 7DGY 1 TITLE COMPND JRNL REVDAT 2 16-FEB-22 7DGY 1 JRNL REVDAT 1 15-DEC-21 7DGY 0 JRNL AUTH B.HUANG,Y.XU,X.HU,Y.LIU,S.LIAO,J.ZHANG,C.HUANG,J.HONG, JRNL AUTH 2 Q.CHEN,H.LIU JRNL TITL A BACKBONE-CENTRED ENERGY FUNCTION OF NEURAL NETWORKS FOR JRNL TITL 2 PROTEIN DESIGN. JRNL REF NATURE V. 602 523 2022 JRNL REFN ESSN 1476-4687 JRNL PMID 35140398 JRNL DOI 10.1038/S41586-021-04383-5 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15624 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1563 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 47.6600 - 4.0100 1.00 1397 156 0.1801 0.1834 REMARK 3 2 4.0100 - 3.1800 1.00 1311 146 0.1708 0.1828 REMARK 3 3 3.1800 - 2.7800 1.00 1288 143 0.1822 0.1919 REMARK 3 4 2.7800 - 2.5300 1.00 1271 140 0.1795 0.2142 REMARK 3 5 2.5300 - 2.3400 1.00 1269 142 0.1810 0.2146 REMARK 3 6 2.3400 - 2.2100 1.00 1270 142 0.1611 0.1909 REMARK 3 7 2.2100 - 2.1000 1.00 1260 138 0.1618 0.1719 REMARK 3 8 2.1000 - 2.0000 1.00 1251 140 0.1706 0.1709 REMARK 3 9 2.0000 - 1.9300 1.00 1253 140 0.1829 0.2510 REMARK 3 10 1.9300 - 1.8600 1.00 1238 137 0.1778 0.2253 REMARK 3 11 1.8600 - 1.8000 1.00 1253 139 0.1897 0.2366 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.50 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -7.1633 22.8074 -15.5066 REMARK 3 T TENSOR REMARK 3 T11: 0.2337 T22: 0.2447 REMARK 3 T33: 0.2656 T12: 0.0196 REMARK 3 T13: 0.0045 T23: 0.0029 REMARK 3 L TENSOR REMARK 3 L11: 1.4347 L22: 1.4800 REMARK 3 L33: 0.2118 L12: 0.6747 REMARK 3 L13: 0.2141 L23: -0.2319 REMARK 3 S TENSOR REMARK 3 S11: -0.0615 S12: -0.0896 S13: -0.0054 REMARK 3 S21: -0.0733 S22: 0.0012 S23: -0.1414 REMARK 3 S31: 0.0138 S32: -0.0105 S33: -0.0001 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 7DGY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1300019365. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15624 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 49.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 25.30 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 45.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.69200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.1 M AMMONIUM TARTRATE DIBASIC, 0.1 M REMARK 280 SODIUM ACETATE TRIHYDRATE, PH 4.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 32.27000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.34100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.34100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.13500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.34100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.34100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 48.40500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.34100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.34100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 16.13500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.34100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.34100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 48.40500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 32.27000 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: MONOMERIC 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 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 A 270 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 280 LIES ON A SPECIAL POSITION. 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 -1 REMARK 465 HIS A 99 REMARK 465 HIS A 100 REMARK 465 HIS A 101 REMARK 465 HIS A 102 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 GLU A 51 CG CD OE1 OE2 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 281 DISTANCE = 6.69 ANGSTROMS DBREF 7DGY A -1 102 PDB 7DGY 7DGY -1 102 SEQRES 1 A 104 MET GLY HIS PRO GLU ILE VAL ALA ALA ALA VAL ALA PHE SEQRES 2 A 104 VAL ARG GLN ILE TRP GLU TYR ALA ARG GLN GLY MET SER SEQRES 3 A 104 LEU ASP GLU MET ILE ALA TRP ALA VAL LYS TYR ALA LYS SEQRES 4 A 104 LYS ILE PHE ASP LEU VAL LYS LYS MET GLY ALA SER ASP SEQRES 5 A 104 GLU VAL LEU LYS LYS VAL MET ASP ALA VAL LEU ALA ALA SEQRES 6 A 104 ALA GLN ALA TYR ALA GLN GLN LEU ASN ASP GLU ALA ALA SEQRES 7 A 104 GLN ARG LEU LEU VAL ALA ALA GLN VAL ILE VAL GLN VAL SEQRES 8 A 104 LEU GLN GLN LEU GLY LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *81(H2 O) HELIX 1 AA1 HIS A 1 GLN A 21 1 21 HELIX 2 AA2 SER A 24 MET A 46 1 23 HELIX 3 AA3 SER A 49 GLN A 69 1 21 HELIX 4 AA4 ASN A 72 HIS A 98 1 27 CRYST1 70.682 70.682 64.540 90.00 90.00 90.00 P 41 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 0.014148 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014148 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015494 0.00000