HEADER DE NOVO PROTEIN 12-SEP-23 8U5A TITLE IMPROVING PROTEIN EXPRESSION, STABILITY, AND FUNCTION WITH PROTEINMPNN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGNED MYOGLOBIN; COMPND 3 CHAIN: A, B; 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 PROTEIN EXPRESSION, STABILITY, FUNCTION, PROTEINMPNN, DE NOVO DESIGN, KEYWDS 2 DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.KALVET,A.K.BERA,D.BAKER REVDAT 2 31-JAN-24 8U5A 1 JRNL REVDAT 1 17-JAN-24 8U5A 0 JRNL AUTH K.H.SUMIDA,R.NUNEZ-FRANCO,I.KALVET,S.J.PELLOCK,B.I.M.WICKY, JRNL AUTH 2 L.F.MILLES,J.DAUPARAS,J.WANG,Y.KIPNIS,N.JAMESON,A.KANG, JRNL AUTH 3 J.DE LA CRUZ,B.SANKARAN,A.K.BERA,G.JIMENEZ-OSES,D.BAKER JRNL TITL IMPROVING PROTEIN EXPRESSION, STABILITY, AND FUNCTION WITH JRNL TITL 2 PROTEINMPNN. JRNL REF J.AM.CHEM.SOC. V. 146 2054 2024 JRNL REFN ESSN 1520-5126 JRNL PMID 38194293 JRNL DOI 10.1021/JACS.3C10941 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 22200 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1984 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 42.6400 - 4.8200 0.99 1554 142 0.2219 0.2448 REMARK 3 2 4.8200 - 3.8300 0.98 1483 148 0.1856 0.2093 REMARK 3 3 3.8200 - 3.3400 0.98 1472 146 0.1979 0.2398 REMARK 3 4 3.3400 - 3.0400 0.99 1459 146 0.2398 0.2523 REMARK 3 5 3.0400 - 2.8200 0.98 1443 137 0.2391 0.2794 REMARK 3 6 2.8200 - 2.6500 0.98 1446 144 0.2340 0.2931 REMARK 3 7 2.6500 - 2.5200 0.98 1452 143 0.2463 0.2972 REMARK 3 8 2.5200 - 2.4100 0.98 1447 147 0.2288 0.2875 REMARK 3 9 2.4100 - 2.3200 0.98 1459 138 0.2380 0.2720 REMARK 3 10 2.3200 - 2.2400 0.94 1365 139 0.3103 0.3794 REMARK 3 11 2.2400 - 2.1700 0.97 1423 135 0.2686 0.3326 REMARK 3 12 2.1700 - 2.1100 0.98 1412 137 0.2705 0.2820 REMARK 3 13 2.1100 - 2.0500 0.95 1429 141 0.3296 0.3560 REMARK 3 14 2.0500 - 2.0000 0.96 1372 141 0.3453 0.4006 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.297 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.464 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.71 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 2588 REMARK 3 ANGLE : 0.522 3512 REMARK 3 CHIRALITY : 0.032 366 REMARK 3 PLANARITY : 0.004 446 REMARK 3 DIHEDRAL : 16.569 976 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 8U5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1000277375. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22200 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 42.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.07530 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.99100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.580 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 (%): 43.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 28% W/V REMARK 280 POLYETHYLENE GLYCOL MONOMETHYL ETHER 2,000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, 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 20.83450 REMARK 290 SMTRY3 2 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 -2 REMARK 465 SER A -1 REMARK 465 GLY A 0 REMARK 465 GLY A 150 REMARK 465 GLY A 151 REMARK 465 GLY A 152 REMARK 465 SER A 153 REMARK 465 GLY A 154 REMARK 465 SER A 155 REMARK 465 HIS A 156 REMARK 465 HIS A 157 REMARK 465 TRP A 158 REMARK 465 GLY A 159 REMARK 465 SER A 160 REMARK 465 THR A 161 REMARK 465 HIS A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 MET B -2 REMARK 465 SER B -1 REMARK 465 GLY B 0 REMARK 465 GLY B 150 REMARK 465 GLY B 151 REMARK 465 GLY B 152 REMARK 465 SER B 153 REMARK 465 GLY B 154 REMARK 465 SER B 155 REMARK 465 HIS B 156 REMARK 465 HIS B 157 REMARK 465 TRP B 158 REMARK 465 GLY B 159 REMARK 465 SER B 160 REMARK 465 THR B 161 REMARK 465 HIS B 162 REMARK 465 HIS B 163 REMARK 465 HIS B 164 REMARK 465 HIS B 165 REMARK 465 HIS B 166 REMARK 465 HIS B 167 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 ASP B 18 47.08 -153.22 REMARK 500 PHE B 120 68.75 -113.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 NE2 REMARK 620 2 HEM A 201 NA 77.3 REMARK 620 3 HEM A 201 NB 81.1 89.3 REMARK 620 4 HEM A 201 NC 95.0 172.3 90.2 REMARK 620 5 HEM A 201 ND 92.7 88.9 173.8 90.8 REMARK 620 6 HOH A 309 O 172.2 97.5 93.2 90.3 93.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 94 NE2 REMARK 620 2 HEM B 201 NA 102.3 REMARK 620 3 HEM B 201 NB 80.3 90.7 REMARK 620 4 HEM B 201 NC 75.1 177.4 88.7 REMARK 620 5 HEM B 201 ND 99.4 90.0 179.3 90.6 REMARK 620 N 1 2 3 4 DBREF 8U5A A -2 167 PDB 8U5A 8U5A -2 167 DBREF 8U5A B -2 167 PDB 8U5A 8U5A -2 167 SEQRES 1 A 170 MET SER GLY SER GLU GLU LYS ALA ALA LEU VAL LEU ALA SEQRES 2 A 170 LEU PHE ASP ARG VAL GLU ALA ASP ARG GLU GLU ILE GLY SEQRES 3 A 170 ALA ALA VAL LEU ARG ARG THR PHE GLU GLU HIS PRO GLU SEQRES 4 A 170 THR LEU LYS LYS PHE PRO ARG PHE LEU GLU LEU TYR LYS SEQRES 5 A 170 LYS GLY SER PRO GLU LEU ASP ALA LEU LEU LYS GLU HIS SEQRES 6 A 170 GLY LYS THR VAL LEU ASP ALA LEU ILE GLU ILE ALA ARG SEQRES 7 A 170 LEU ARG TYR SER GLY GLU ASP TYR ARG SER LEU ILE LYS SEQRES 8 A 170 GLU LEU ALA LYS SER HIS LYS GLU GLU HIS LYS ILE PRO SEQRES 9 A 170 ILE GLU ASP LEU ARG HIS ILE ALA GLU ALA LEU LEU ALA SEQRES 10 A 170 VAL LEU ALA GLU ARG PHE PRO ASP GLU PHE GLY PRO GLU SEQRES 11 A 170 ALA ARG ALA ALA LEU THR ASP PHE LEU ASP TRP PHE ILE SEQRES 12 A 170 ALA GLU ILE GLU GLU GLU TYR LYS LYS GLY GLY GLY SER SEQRES 13 A 170 GLY SER HIS HIS TRP GLY SER THR HIS HIS HIS HIS HIS SEQRES 14 A 170 HIS SEQRES 1 B 170 MET SER GLY SER GLU GLU LYS ALA ALA LEU VAL LEU ALA SEQRES 2 B 170 LEU PHE ASP ARG VAL GLU ALA ASP ARG GLU GLU ILE GLY SEQRES 3 B 170 ALA ALA VAL LEU ARG ARG THR PHE GLU GLU HIS PRO GLU SEQRES 4 B 170 THR LEU LYS LYS PHE PRO ARG PHE LEU GLU LEU TYR LYS SEQRES 5 B 170 LYS GLY SER PRO GLU LEU ASP ALA LEU LEU LYS GLU HIS SEQRES 6 B 170 GLY LYS THR VAL LEU ASP ALA LEU ILE GLU ILE ALA ARG SEQRES 7 B 170 LEU ARG TYR SER GLY GLU ASP TYR ARG SER LEU ILE LYS SEQRES 8 B 170 GLU LEU ALA LYS SER HIS LYS GLU GLU HIS LYS ILE PRO SEQRES 9 B 170 ILE GLU ASP LEU ARG HIS ILE ALA GLU ALA LEU LEU ALA SEQRES 10 B 170 VAL LEU ALA GLU ARG PHE PRO ASP GLU PHE GLY PRO GLU SEQRES 11 B 170 ALA ARG ALA ALA LEU THR ASP PHE LEU ASP TRP PHE ILE SEQRES 12 B 170 ALA GLU ILE GLU GLU GLU TYR LYS LYS GLY GLY GLY SER SEQRES 13 B 170 GLY SER HIS HIS TRP GLY SER THR HIS HIS HIS HIS HIS SEQRES 14 B 170 HIS HET HEM A 201 43 HET HEM B 201 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 HOH *85(H2 O) HELIX 1 AA1 SER A 1 ASP A 18 1 18 HELIX 2 AA2 ASP A 18 HIS A 34 1 17 HELIX 3 AA3 HIS A 34 LYS A 40 1 7 HELIX 4 AA4 PHE A 41 LYS A 50 1 10 HELIX 5 AA5 GLU A 54 TYR A 78 1 25 HELIX 6 AA6 TYR A 83 GLU A 96 1 14 HELIX 7 AA7 PRO A 101 PHE A 120 1 20 HELIX 8 AA8 GLY A 125 LYS A 148 1 24 HELIX 9 AA9 GLU B 2 ALA B 17 1 16 HELIX 10 AB1 ASP B 18 HIS B 34 1 17 HELIX 11 AB2 HIS B 34 LYS B 40 1 7 HELIX 12 AB3 PHE B 41 LYS B 50 1 10 HELIX 13 AB4 GLU B 54 SER B 79 1 26 HELIX 14 AB5 TYR B 83 GLU B 96 1 14 HELIX 15 AB6 PRO B 101 PHE B 120 1 20 HELIX 16 AB7 GLY B 125 LYS B 148 1 24 LINK NE2 HIS A 94 FE HEM A 201 1555 1555 2.61 LINK FE HEM A 201 O HOH A 309 1555 1555 2.10 LINK NE2 HIS B 94 FE HEM B 201 1555 1555 2.02 CRYST1 31.589 41.669 128.439 90.00 95.13 90.00 P 1 21 1 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 0.031657 0.000000 0.002842 0.00000 SCALE2 0.000000 0.023999 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007817 0.00000