HEADER DE NOVO PROTEIN 17-MAY-21 7MWR TITLE STRUCTURE OF DE NOVO DESIGNED BETA SHEET HETERODIMER LHD101A53/B4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LHD101A54; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LHD101B4; 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 DE NOVO DESIGN, BETA-SHEET, HETERODIMER, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,D.D.SAHTOE,A.KANG,F.PRAETORIUS,D.BAKER REVDAT 4 03-APR-24 7MWR 1 REMARK REVDAT 3 16-FEB-22 7MWR 1 TITLE REVDAT 2 02-FEB-22 7MWR 1 JRNL REVDAT 1 19-JAN-22 7MWR 0 JRNL AUTH D.D.SAHTOE,F.PRAETORIUS,A.COURBET,Y.HSIA,B.I.M.WICKY, JRNL AUTH 2 N.I.EDMAN,L.M.MILLER,B.J.R.TIMMERMANS,J.DECARREAU, JRNL AUTH 3 H.M.MORRIS,A.KANG,A.K.BERA,D.BAKER JRNL TITL RECONFIGURABLE ASYMMETRIC PROTEIN ASSEMBLIES THROUGH JRNL TITL 2 IMPLICIT NEGATIVE DESIGN. JRNL REF SCIENCE V. 375 J7662 2022 JRNL REFN ESSN 1095-9203 JRNL PMID 35050655 JRNL DOI 10.1126/SCIENCE.ABJ7662 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 29009 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1440 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 46.1800 - 4.7300 1.00 2973 136 0.1956 0.2010 REMARK 3 2 4.7300 - 3.7600 1.00 2807 140 0.1730 0.2100 REMARK 3 3 3.7600 - 3.2800 1.00 2776 145 0.1897 0.2478 REMARK 3 4 3.2800 - 2.9800 1.00 2752 144 0.2197 0.2945 REMARK 3 5 2.9800 - 2.7700 1.00 2727 146 0.2278 0.3213 REMARK 3 6 2.7700 - 2.6100 1.00 2731 144 0.2384 0.2844 REMARK 3 7 2.6100 - 2.4700 1.00 2747 147 0.2412 0.2952 REMARK 3 8 2.4700 - 2.3700 1.00 2682 152 0.2481 0.2826 REMARK 3 9 2.3700 - 2.2800 1.00 2704 134 0.2817 0.3186 REMARK 3 10 2.2800 - 2.2000 0.98 2670 152 0.4071 0.4016 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.473 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.72 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.43 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 : 0.002 3540 REMARK 3 ANGLE : 0.401 4758 REMARK 3 CHIRALITY : 0.037 573 REMARK 3 PLANARITY : 0.003 621 REMARK 3 DIHEDRAL : 14.226 1414 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 7MWR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1000256950. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29009 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 46.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.03100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 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) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: DESIGN MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4M SODIUM MALONATE PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.70450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.04700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.88750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.04700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.70450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.88750 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 64 28.01 -77.58 REMARK 500 ASN A 155 -46.54 70.76 REMARK 500 VAL B 193 -168.28 -111.29 REMARK 500 SER B 200 -167.01 -104.78 REMARK 500 REMARK 500 REMARK: NULL DBREF 7MWR A -1 202 PDB 7MWR 7MWR -1 202 DBREF 7MWR B 1 249 PDB 7MWR 7MWR 1 249 SEQRES 1 A 204 GLY SER ASN ASP GLU LYS GLU LYS LEU LYS GLU LEU LEU SEQRES 2 A 204 LYS ARG ALA GLU GLU LEU ALA LYS SER PRO ASP PRO GLU SEQRES 3 A 204 ASP LEU LYS GLU ALA VAL ARG LEU ALA GLU GLU VAL VAL SEQRES 4 A 204 ARG GLU ARG PRO GLY SER ASN LEU ALA LYS LYS ALA LEU SEQRES 5 A 204 GLU ILE ILE LEU ARG ALA ALA GLU GLU LEU ALA LYS LEU SEQRES 6 A 204 PRO ASP PRO GLU ALA LEU LYS GLU ALA VAL LYS ALA ALA SEQRES 7 A 204 GLU LYS VAL VAL ARG GLU GLN PRO GLY SER ASN LEU ALA SEQRES 8 A 204 LYS LYS ALA LEU GLU ILE ILE LEU ARG ALA ALA ALA ALA SEQRES 9 A 204 LEU ALA ASN LEU PRO ASP PRO GLU SER ARG LYS GLU ALA SEQRES 10 A 204 ASP LYS ALA ALA ASP LYS VAL ARG ARG GLU GLN PRO GLY SEQRES 11 A 204 SER GLU LEU ALA VAL VAL ALA ALA ILE ILE SER ALA VAL SEQRES 12 A 204 ALA ARG MET GLY VAL LYS MET GLU LEU HIS PRO SER GLY SEQRES 13 A 204 ASN GLU VAL LYS VAL VAL ILE LYS GLY LEU HIS ILE LYS SEQRES 14 A 204 GLN GLN ARG GLN LEU TYR ARG ASP VAL ARG GLU ALA ALA SEQRES 15 A 204 LYS LYS ALA GLY VAL GLU VAL GLU ILE GLU VAL GLU GLY SEQRES 16 A 204 ASP THR VAL THR ILE VAL VAL ARG GLY SEQRES 1 B 249 TYR GLU ASP GLU CYS GLU GLU LYS ALA ARG ARG VAL ALA SEQRES 2 B 249 GLU LYS VAL GLU ARG LEU LYS ARG SER GLY THR SER GLU SEQRES 3 B 249 ASP GLU ILE ALA GLU GLU VAL ALA ARG GLU ILE SER GLU SEQRES 4 B 249 VAL ILE ARG THR LEU LYS GLU SER GLY SER SER TYR GLU SEQRES 5 B 249 VAL ILE CYS GLU CYS VAL ALA ARG ILE VAL ALA GLU ILE SEQRES 6 B 249 VAL GLU ALA LEU LYS ARG SER GLY THR SER GLU ASP GLU SEQRES 7 B 249 ILE ALA GLU ILE VAL ALA ARG VAL ILE SER GLU VAL ILE SEQRES 8 B 249 ARG THR LEU LYS GLU SER GLY SER SER TYR GLU VAL ILE SEQRES 9 B 249 CYS GLU CYS VAL ALA ARG ILE VAL ALA GLU ILE VAL GLU SEQRES 10 B 249 ALA LEU LYS ARG SER GLY THR SER GLU GLU GLU ILE ALA SEQRES 11 B 249 GLU ILE VAL ALA ARG VAL ILE GLN GLU VAL ILE ARG THR SEQRES 12 B 249 LEU LYS GLU SER GLY SER SER TYR GLU VAL ILE ARG GLU SEQRES 13 B 249 CYS LEU ARG ARG ILE LEU GLU GLU VAL ILE GLU ALA LEU SEQRES 14 B 249 LYS ARG SER GLY VAL ASP SER SER GLU ILE VAL LEU ILE SEQRES 15 B 249 ILE ILE LYS ILE ALA VAL ALA VAL MET GLY VAL THR MET SEQRES 16 B 249 GLU GLU HIS ARG SER GLY ASN GLU VAL LYS VAL VAL ILE SEQRES 17 B 249 LYS GLY LEU HIS GLU SER GLN GLN GLU GLU LEU LEU GLU SEQRES 18 B 249 LEU VAL LEU ARG ALA ALA GLU LEU ALA GLY VAL ARG VAL SEQRES 19 B 249 ARG ILE ARG PHE LYS GLY ASP THR VAL THR ILE VAL VAL SEQRES 20 B 249 ARG GLY HET MLI A 301 7 HETNAM MLI MALONATE ION FORMUL 3 MLI C3 H2 O4 2- FORMUL 4 HOH *82(H2 O) HELIX 1 AA1 SER A 0 ALA A 18 1 19 HELIX 2 AA2 ASP A 22 ARG A 40 1 19 HELIX 3 AA3 SER A 43 ALA A 61 1 19 HELIX 4 AA4 ASP A 65 GLN A 83 1 19 HELIX 5 AA5 SER A 86 ASN A 105 1 20 HELIX 6 AA6 ASP A 108 GLU A 125 1 18 HELIX 7 AA7 SER A 129 GLY A 145 1 17 HELIX 8 AA8 HIS A 165 ALA A 183 1 19 HELIX 9 AA9 GLU B 2 SER B 22 1 21 HELIX 10 AB1 SER B 25 SER B 47 1 23 HELIX 11 AB2 SER B 50 SER B 72 1 23 HELIX 12 AB3 SER B 75 SER B 97 1 23 HELIX 13 AB4 SER B 100 GLY B 123 1 24 HELIX 14 AB5 SER B 125 SER B 147 1 23 HELIX 15 AB6 SER B 150 SER B 172 1 23 HELIX 16 AB7 ASP B 175 GLY B 192 1 18 HELIX 17 AB8 HIS B 212 GLY B 231 1 20 SHEET 1 AA1 8 LYS A 147 PRO A 152 0 SHEET 2 AA1 8 GLU A 156 LYS A 162 -1 O LYS A 158 N HIS A 151 SHEET 3 AA1 8 THR A 195 ARG A 201 -1 O ILE A 198 N VAL A 159 SHEET 4 AA1 8 GLU A 186 GLU A 192 -1 N GLU A 190 O THR A 197 SHEET 5 AA1 8 ARG B 233 LYS B 239 -1 O PHE B 238 N ILE A 189 SHEET 6 AA1 8 THR B 242 ARG B 248 -1 O VAL B 246 N ARG B 235 SHEET 7 AA1 8 GLU B 203 LYS B 209 -1 N VAL B 206 O ILE B 245 SHEET 8 AA1 8 THR B 194 ARG B 199 -1 N HIS B 198 O LYS B 205 SSBOND 1 CYS B 5 CYS B 57 1555 1555 2.03 SSBOND 2 CYS B 55 CYS B 107 1555 1555 2.03 SSBOND 3 CYS B 105 CYS B 157 1555 1555 2.03 CRYST1 45.409 99.775 122.094 90.00 90.00 90.00 P 21 21 21 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 0.022022 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010023 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008190 0.00000