HEADER DE NOVO PROTEIN 06-MAR-24 8S89 TITLE EFFICIENT AND SCALABLE PROTEIN DESIGN USING A RELAXED SEQUENCE SPACE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO PROTEIN P400; COMPND 3 CHAIN: A; COMPND 4 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 KEYWDS DE NOVO PROTEIN, P400 EXPDTA X-RAY DIFFRACTION AUTHOR C.J.FRANK,H.DIETZ REVDAT 1 16-OCT-24 8S89 0 JRNL AUTH C.J.FRANK,H.DIETZ JRNL TITL EFFICIENT AND SCALABLE PROTEIN DESIGN USING A RELAXED JRNL TITL 2 SEQUENCE SPACE JRNL REF SCIENCE 2024 JRNL REFN ESSN 1095-9203 JRNL DOI 10.1126/SCIENCE.ADQ1741 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.1_3865 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25154 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 1303 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 43.2400 - 4.3700 1.00 2686 170 0.1749 0.1731 REMARK 3 2 4.3700 - 3.4700 1.00 2666 143 0.1793 0.2276 REMARK 3 3 3.4700 - 3.0300 1.00 2681 138 0.2193 0.2778 REMARK 3 4 3.0300 - 2.7500 1.00 2618 147 0.2361 0.2935 REMARK 3 5 2.7500 - 2.5500 1.00 2644 145 0.2253 0.2918 REMARK 3 6 2.5500 - 2.4000 1.00 2650 141 0.2240 0.2964 REMARK 3 7 2.4000 - 2.2800 1.00 2638 139 0.2189 0.2568 REMARK 3 8 2.2800 - 2.1800 1.00 2647 123 0.2297 0.2883 REMARK 3 9 2.1800 - 2.1000 1.00 2621 157 0.2675 0.2864 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) : 0.206 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.32 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 : 0.010 3103 REMARK 3 ANGLE : 1.207 4213 REMARK 3 CHIRALITY : 0.059 514 REMARK 3 PLANARITY : 0.006 542 REMARK 3 DIHEDRAL : 25.677 1136 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 8S89 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1292136874. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-23 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 : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25154 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.10260 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.67930 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 MMOL MAGNESIUM SULFATE, 28-32% REMARK 280 PEG4000, 0.1 M TRIS PH 8.5-9.3, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 31.29550 REMARK 290 SMTRY3 2 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: 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 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 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 750 O HOH A 766 2.05 REMARK 500 O HOH A 649 O HOH A 758 2.07 REMARK 500 O HOH A 746 O HOH A 765 2.13 REMARK 500 O HOH A 664 O HOH A 732 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 744 O HOH A 748 2656 2.11 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 40 -66.05 -101.81 REMARK 500 PHE A 66 -148.98 -131.18 REMARK 500 REMARK 500 REMARK: NULL 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 775 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 776 DISTANCE = 6.29 ANGSTROMS DBREF 8S89 A 0 401 PDB 8S89 8S89 0 401 SEQRES 1 A 402 MET SER LYS ALA GLU LEU ALA ALA MET SER GLU ALA GLU SEQRES 2 A 402 PHE ARG ALA LEU LEU GLN GLY LYS LYS GLU THR LEU LYS SEQRES 3 A 402 ASN ILE ILE LYS GLU LEU ASP GLU LYS ILE LYS GLU LEU SEQRES 4 A 402 LEU GLU GLU HIS PRO ASP LEU SER LEU GLU GLU LYS LEU SEQRES 5 A 402 ALA GLU LEU LEU ARG PHE PHE VAL GLU VAL PHE SER LYS SEQRES 6 A 402 ASN PHE SER PRO GLU ALA ALA VAL THR PHE TYR GLN ASN SEQRES 7 A 402 PHE TYR GLU LEU LEU ARG THR TYR ALA ALA VAL LEU HIS SEQRES 8 A 402 GLY GLU GLU ALA VAL PRO PRO PRO LEU VAL MET THR PRO SEQRES 9 A 402 GLU LEU ALA ALA GLU ILE ILE ALA LEU PHE GLN ALA ALA SEQRES 10 A 402 THR GLU SER GLU GLU GLY LEU GLU ALA PHE ILE ALA PHE SEQRES 11 A 402 VAL LEU GLY ASP PRO ALA LEU GLN LYS LEU ILE ASP MET SEQRES 12 A 402 LEU GLY LYS ASP LYS VAL VAL ILE LEU SER LEU PHE ALA SEQRES 13 A 402 ILE ALA PHE ILE LYS THR ALA VAL ASP SER ALA LEU GLU SEQRES 14 A 402 GLU ALA ASP LYS LEU GLY ALA ALA ALA LEU GLU LEU ALA SEQRES 15 A 402 GLU GLU ASN ARG GLY THR ALA GLU GLY GLU ARG HIS LEU SEQRES 16 A 402 GLN PHE TYR ALA ALA THR GLN GLY LEU LYS ALA TRP LEU SEQRES 17 A 402 LYS GLU LEU GLU ILE THR GLU THR THR LYS ILE PHE ASP SEQRES 18 A 402 ASP LEU ILE GLU GLU ARG PRO GLU LEU ALA ALA GLU LEU SEQRES 19 A 402 GLU ALA VAL ARG ASP ARG VAL MET GLY ALA LEU LEU ASP SEQRES 20 A 402 GLU VAL LEU ALA GLU VAL ASP ALA THR VAL ALA ALA VAL SEQRES 21 A 402 LEU ALA ARG LEU ARG ALA LEU ALA GLU ALA LEU ASP PRO SEQRES 22 A 402 LYS VAL ARG LEU THR SER VAL ALA VAL GLU VAL ALA TRP SEQRES 23 A 402 THR GLU ASP GLY LEU LEU THR VAL THR VAL ASP VAL ARG SEQRES 24 A 402 THR GLU SER GLY PRO LEU GLY ALA THR PRO GLU GLU ILE SEQRES 25 A 402 ALA GLU ALA GLN TRP ALA ILE SER ARG LEU LEU ALA THR SEQRES 26 A 402 ALA ALA ALA GLU LEU SER ALA LEU GLU ARG VAL LEU GLU SEQRES 27 A 402 THR LEU LEU LYS HIS VAL ALA GLU ALA ASP LYS ALA ARG SEQRES 28 A 402 VAL GLU ALA ALA LEU ALA ARG VAL GLU THR THR ARG ALA SEQRES 29 A 402 GLY LEU ILE ASP ILE PHE ARG GLU ALA ALA ALA ALA GLN SEQRES 30 A 402 ALA ALA GLY SER PRO ARG THR LEU ALA GLU ILE ALA ALA SEQRES 31 A 402 ALA ARG LEU ALA ALA LEU LEU ALA ALA LEU ALA GLY HET SO4 A 501 5 HET SO4 A 502 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *176(H2 O) HELIX 1 AA1 SER A 1 MET A 8 1 8 HELIX 2 AA2 SER A 9 HIS A 42 1 34 HELIX 3 AA3 SER A 46 PHE A 66 1 21 HELIX 4 AA4 PRO A 68 GLY A 91 1 24 HELIX 5 AA5 THR A 102 THR A 117 1 16 HELIX 6 AA6 SER A 119 ASP A 133 1 15 HELIX 7 AA7 ASP A 133 LEU A 143 1 11 HELIX 8 AA8 ASP A 146 ASN A 184 1 39 HELIX 9 AA9 THR A 187 ARG A 226 1 40 HELIX 10 AB1 LEU A 229 LEU A 270 1 42 HELIX 11 AB2 THR A 307 LYS A 341 1 35 HELIX 12 AB3 ALA A 344 ALA A 346 5 3 HELIX 13 AB4 ASP A 347 ALA A 378 1 32 HELIX 14 AB5 THR A 383 GLY A 401 1 19 SHEET 1 AA1 2 LEU A 276 TRP A 285 0 SHEET 2 AA1 2 LEU A 291 THR A 299 -1 O ARG A 298 N SER A 278 CRYST1 43.596 62.591 80.269 90.00 97.35 90.00 P 1 21 1 2 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 0.022938 0.000000 0.002960 0.00000 SCALE2 0.000000 0.015977 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012561 0.00000