HEADER DE NOVO PROTEIN 13-DEC-23 8VC8 TITLE CRYSTAL STRUCTURE OF HEME-LOADED DESIGN: HEM_3.C9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEM_3.C9; 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 DESIGN, RFDIFFUSION, ALPHAFOLD2, ROSETTAFOLD, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.KALVET,A.K.BERA,D.BAKER REVDAT 2 01-MAY-24 8VC8 1 JRNL REVDAT 1 20-MAR-24 8VC8 0 JRNL AUTH R.KRISHNA,J.WANG,W.AHERN,P.STURMFELS,P.VENKATESH,I.KALVET, JRNL AUTH 2 G.R.LEE,F.S.MOREY-BURROWS,I.ANISHCHENKO,I.R.HUMPHREYS, JRNL AUTH 3 R.MCHUGH,D.VAFEADOS,X.LI,G.A.SUTHERLAND,A.HITCHCOCK, JRNL AUTH 4 C.N.HUNTER,A.KANG,E.BRACKENBROUGH,A.K.BERA,M.BAEK,F.DIMAIO, JRNL AUTH 5 D.BAKER JRNL TITL GENERALIZED BIOMOLECULAR MODELING AND DESIGN WITH JRNL TITL 2 ROSETTAFOLD ALL-ATOM. JRNL REF SCIENCE V. 384 L2528 2024 JRNL REFN ESSN 1095-9203 JRNL PMID 38452047 JRNL DOI 10.1126/SCIENCE.ADL2528 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_4761 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.090 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 16611 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1650 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 28.0600 - 4.1200 0.99 1413 157 0.1798 0.2103 REMARK 3 2 4.1200 - 3.2700 0.99 1317 149 0.1754 0.2158 REMARK 3 3 3.2700 - 2.8600 0.98 1293 137 0.1911 0.2307 REMARK 3 4 2.8600 - 2.6000 0.99 1296 146 0.1883 0.2656 REMARK 3 5 2.6000 - 2.4100 0.97 1257 147 0.1797 0.2019 REMARK 3 6 2.4100 - 2.2700 0.98 1264 134 0.1709 0.2097 REMARK 3 7 2.2700 - 2.1500 0.97 1256 139 0.1715 0.2393 REMARK 3 8 2.1500 - 2.0600 0.94 1214 140 0.1943 0.2639 REMARK 3 9 2.0600 - 1.9800 0.92 1162 122 0.2138 0.3064 REMARK 3 10 1.9800 - 1.9100 0.92 1187 136 0.2440 0.2836 REMARK 3 11 1.9100 - 1.8500 0.91 1180 123 0.2733 0.3151 REMARK 3 12 1.8500 - 1.8000 0.89 1122 120 0.3218 0.3409 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) : 0.215 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.805 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.39 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 : 0.015 1576 REMARK 3 ANGLE : 1.395 2140 REMARK 3 CHIRALITY : 0.081 238 REMARK 3 PLANARITY : 0.009 272 REMARK 3 DIHEDRAL : 16.523 595 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): 1.8017 16.1136 15.0080 REMARK 3 T TENSOR REMARK 3 T11: 0.1769 T22: 0.1368 REMARK 3 T33: 0.1593 T12: -0.0056 REMARK 3 T13: -0.0114 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 2.5494 L22: 1.0528 REMARK 3 L33: 1.7773 L12: 0.4398 REMARK 3 L13: -0.1914 L23: 0.2023 REMARK 3 S TENSOR REMARK 3 S11: 0.0112 S12: 0.1044 S13: 0.0868 REMARK 3 S21: 0.0300 S22: 0.0102 S23: -0.0304 REMARK 3 S31: -0.0988 S32: 0.0682 S33: -0.0048 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 8VC8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1000279903. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92009 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16611 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 28.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8400 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) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.010 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 (%): 39.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2M AMMONIUM SULFATE, 0.1M CITRATE PH REMARK 280 5, VAPOR 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 18.99350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.61950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.81100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.61950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.99350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.81100 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: 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 -1 REMARK 465 SER A 0 REMARK 465 GLY A 198 REMARK 465 SER A 199 REMARK 465 HIS A 200 REMARK 465 HIS A 201 REMARK 465 TRP A 202 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 454 O HOH A 455 2.03 REMARK 500 O HOH A 455 O HOH A 457 2.13 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 PRO A 88 55.43 -69.78 REMARK 500 GLU A 90 -138.14 -173.37 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 302 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 141 SG REMARK 620 2 HEM A 302 NA 98.2 REMARK 620 3 HEM A 302 NB 95.8 89.6 REMARK 620 4 HEM A 302 NC 98.6 163.1 87.0 REMARK 620 5 HEM A 302 ND 101.3 86.1 162.7 92.4 REMARK 620 N 1 2 3 4 DBREF 8VC8 A -1 202 PDB 8VC8 8VC8 -1 202 SEQRES 1 A 204 MET SER GLY SER ILE GLU GLU LEU ALA LYS ILE ALA LYS SEQRES 2 A 204 LYS ILE ALA GLU GLU LEU TYR PRO GLU ILE LEU LYS GLU SEQRES 3 A 204 VAL GLY ASP GLU GLU PHE ALA GLU LYS LEU SER ARG GLY SEQRES 4 A 204 LEU ALA ILE ALA GLY VAL ALA LEU ALA VAL ALA GLY VAL SEQRES 5 A 204 PRO LEU GLU GLU ILE VAL LYS ALA SER PRO GLU GLN VAL SEQRES 6 A 204 LYS GLU LEU GLU PRO LEU PHE GLU LYS ALA GLY ARG ILE SEQRES 7 A 204 GLU ALA GLN ILE ALA GLN VAL LEU THR GLY GLU PRO GLU SEQRES 8 A 204 GLU ASP LEU GLU LYS ALA ALA LYS ALA VAL ALA ALA GLY SEQRES 9 A 204 ALA TYR PHE GLY ALA LEU VAL ILE ALA GLY VAL PRO PHE SEQRES 10 A 204 GLU GLU ALA ALA LYS GLU VAL ALA LYS PHE LEU GLU GLY SEQRES 11 A 204 LEU THR PRO GLU GLU ILE ALA ARG PHE ALA GLN ARG CYS SEQRES 12 A 204 PRO ALA LEU VAL LYS ALA ALA PRO GLU ILE LEU LYS ARG SEQRES 13 A 204 ASP SER ILE THR PRO GLU GLU PHE ALA LYS LEU LEU ILE SEQRES 14 A 204 GLU HIS LYS GLU GLU LEU LEU GLU LEU GLY ARG LEU GLY SEQRES 15 A 204 LEU PRO TYR LEU LEU LYS ALA TYR LYS MET ALA LYS GLU SEQRES 16 A 204 LEU LEU GLY SER GLY SER HIS HIS TRP HET SO4 A 301 5 HET HEM A 302 43 HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 SO4 O4 S 2- FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 HOH *62(H2 O) HELIX 1 AA1 SER A 2 VAL A 25 1 24 HELIX 2 AA2 ASP A 27 GLY A 49 1 23 HELIX 3 AA3 PRO A 51 VAL A 56 1 6 HELIX 4 AA4 SER A 59 LEU A 66 1 8 HELIX 5 AA5 LEU A 66 GLY A 86 1 21 HELIX 6 AA6 ASP A 91 GLY A 112 1 22 HELIX 7 AA7 PRO A 114 GLU A 127 1 14 HELIX 8 AA8 THR A 130 GLN A 139 1 10 HELIX 9 AA9 CYS A 141 ALA A 148 1 8 HELIX 10 AB1 PRO A 149 ARG A 154 5 6 HELIX 11 AB2 THR A 158 HIS A 169 1 12 HELIX 12 AB3 HIS A 169 SER A 197 1 29 LINK SG CYS A 141 FE HEM A 302 1555 1555 2.37 CRYST1 37.987 39.622 119.239 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 0.026325 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025239 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008387 0.00000