HEADER BIOSYNTHETIC PROTEIN 29-DEC-22 8C3W TITLE CRYSTAL STRUCTURE OF A COMPUTATIONALLY DESIGNED HEME BINDING PROTEIN, TITLE 2 DNHEM1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNHEM1; 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, COMPUTATIONAL DESIGN, HEME BINDING PROTEIN, KEYWDS 2 BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.ORTMAYER,C.LEVY REVDAT 4 07-FEB-24 8C3W 1 REMARK REVDAT 3 20-SEP-23 8C3W 1 REMARK REVDAT 2 19-JUL-23 8C3W 1 JRNL REMARK REVDAT 1 05-JUL-23 8C3W 0 JRNL AUTH I.KALVET,M.ORTMAYER,J.ZHAO,R.CRAWSHAW,N.M.ENNIST,C.LEVY, JRNL AUTH 2 A.ROY,A.P.GREEN,D.BAKER JRNL TITL DESIGN OF HEME ENZYMES WITH A TUNABLE SUBSTRATE BINDING JRNL TITL 2 POCKET ADJACENT TO AN OPEN METAL COORDINATION SITE. JRNL REF J.AM.CHEM.SOC. V. 145 14307 2023 JRNL REFN ESSN 1520-5126 JRNL PMID 37341421 JRNL DOI 10.1021/JACS.3C02742 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.V.AFONINE,R.W.GROSSE-KUNSTLEVE,N.ECHOLS,J.J.HEADD, REMARK 1 AUTH 2 N.W.MORIARTY,M.MUSTYAKIMOV,T.C.TERWILLIGER,A.URZHUMTSEV, REMARK 1 AUTH 3 P.H.ZWART,P.D.ADAMS REMARK 1 TITL TOWARDS AUTOMATED CRYSTALLOGRAPHIC STRUCTURE REFINEMENT WITH REMARK 1 TITL 2 PHENIX.REFINE. REMARK 1 REF ACTA CRYSTALLOGR D BIOL V. 68 352 2012 REMARK 1 REF 2 CRYSTALLOGR REMARK 1 REFN ESSN 1399-0047 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 31355 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 1488 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 41.6600 - 3.5600 1.00 2957 139 0.1843 0.1955 REMARK 3 2 3.5600 - 2.8200 1.00 2807 135 0.1706 0.1857 REMARK 3 3 2.8200 - 2.4700 0.99 2760 139 0.1619 0.1703 REMARK 3 4 2.4700 - 2.2400 0.99 2698 174 0.1628 0.1781 REMARK 3 5 2.2400 - 2.0800 0.99 2744 128 0.1763 0.2141 REMARK 3 6 2.0800 - 1.9600 0.99 2712 138 0.1864 0.2390 REMARK 3 7 1.9600 - 1.8600 0.98 2702 119 0.1925 0.2326 REMARK 3 8 1.8600 - 1.7800 0.98 2682 136 0.2095 0.2357 REMARK 3 9 1.7800 - 1.7100 0.98 2664 143 0.2319 0.2684 REMARK 3 10 1.7100 - 1.6500 0.96 2645 121 0.2704 0.2835 REMARK 3 11 1.6500 - 1.6000 0.92 2496 116 0.3234 0.3386 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.65 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 : 0.011 1665 REMARK 3 ANGLE : 1.141 2270 REMARK 3 CHIRALITY : 0.049 304 REMARK 3 PLANARITY : 0.010 260 REMARK 3 DIHEDRAL : 12.809 247 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 8C3W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1292127697. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-22 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31364 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 41.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : 0.05610 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.70 REMARK 200 R MERGE FOR SHELL (I) : 1.03600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.330 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: 4YXX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.7, 70% (4S)-2-METHYL REMARK 280 -2,4-PENTANEDIOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 25.87600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.10200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.57950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.10200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.87600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.57950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL 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 465 GLY A 212 REMARK 465 SER A 213 REMARK 465 GLY A 214 REMARK 465 GLY A 215 REMARK 465 SER A 216 REMARK 465 HIS A 217 REMARK 465 HIS A 218 REMARK 465 TRP A 219 REMARK 465 GLY A 220 REMARK 465 SER A 221 REMARK 465 GLY A 222 REMARK 465 SER A 223 REMARK 465 HIS A 224 REMARK 465 HIS A 225 REMARK 465 HIS A 226 REMARK 465 HIS A 227 REMARK 465 HIS A 228 REMARK 465 HIS A 229 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 HIS A 148 NE2 REMARK 620 2 HEM A 302 NA 91.2 REMARK 620 3 HEM A 302 NB 90.4 90.3 REMARK 620 4 HEM A 302 NC 91.6 176.9 91.1 REMARK 620 5 HEM A 302 ND 90.0 90.8 178.8 87.8 REMARK 620 6 IMD A 301 N1 176.9 92.0 89.4 85.3 90.1 REMARK 620 N 1 2 3 4 5 DBREF 8C3W A 0 229 PDB 8C3W 8C3W 0 229 SEQRES 1 A 230 MET VAL SER LEU ASP GLN ALA ILE LEU ILE LEU VAL VAL SEQRES 2 A 230 ALA ALA LYS LEU GLY THR THR VAL GLU GLU ALA VAL LYS SEQRES 3 A 230 ARG ALA LEU TRP LEU LYS THR LYS LEU GLY VAL SER LEU SEQRES 4 A 230 ASP GLN ALA LEU ARG ILE LEU SER ALA ALA ALA ASN THR SEQRES 5 A 230 GLY THR THR VAL GLU GLU ALA VAL LYS ARG ALA LEU LYS SEQRES 6 A 230 LEU LYS THR LYS LEU GLY VAL SER LEU GLU ALA ALA LEU SEQRES 7 A 230 ALA ILE LEU SER ALA ALA ALA GLN LEU GLY THR THR VAL SEQRES 8 A 230 GLU GLU ALA VAL LYS ARG ALA LEU LYS LEU LYS THR LYS SEQRES 9 A 230 LEU GLY VAL ASP LEU GLU THR ALA ALA LEU ALA LEU LEU SEQRES 10 A 230 THR ALA ALA LYS LEU GLY THR THR VAL GLU GLU ALA VAL SEQRES 11 A 230 LYS ARG ALA LEU LYS LEU LYS THR LYS LEU GLY VAL SER SEQRES 12 A 230 LEU ILE GLU ALA LEU HIS ILE LEU LEU THR ALA ALA VAL SEQRES 13 A 230 LEU GLY THR THR VAL GLU GLU ALA VAL TYR ARG ALA LEU SEQRES 14 A 230 LYS LEU LYS THR LYS LEU GLY VAL SER LEU LEU GLN ALA SEQRES 15 A 230 ALA ALA ILE LEU ILE LEU ALA ALA ARG LEU GLY THR THR SEQRES 16 A 230 VAL GLU GLU ALA VAL LYS ARG ALA LEU LYS LEU LYS THR SEQRES 17 A 230 LYS LEU GLY GLY GLY SER GLY GLY SER HIS HIS TRP GLY SEQRES 18 A 230 SER GLY SER HIS HIS HIS HIS HIS HIS HET IMD A 301 9 HET HEM A 302 73 HET MPD A 303 22 HET PO4 A 304 5 HET PEG A 305 17 HET EDO A 306 10 HET MPD A 307 22 HETNAM IMD IMIDAZOLE HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM PO4 PHOSPHATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EDO 1,2-ETHANEDIOL HETSYN HEM HEME HETSYN EDO ETHYLENE GLYCOL FORMUL 2 IMD C3 H5 N2 1+ FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 MPD 2(C6 H14 O2) FORMUL 5 PO4 O4 P 3- FORMUL 6 PEG C4 H10 O3 FORMUL 7 EDO C2 H6 O2 FORMUL 9 HOH *115(H2 O) HELIX 1 AA1 SER A 2 GLY A 17 1 16 HELIX 2 AA2 THR A 19 GLY A 35 1 17 HELIX 3 AA3 SER A 37 GLY A 52 1 16 HELIX 4 AA4 THR A 54 GLY A 70 1 17 HELIX 5 AA5 SER A 72 GLY A 87 1 16 HELIX 6 AA6 THR A 89 GLY A 105 1 17 HELIX 7 AA7 ASP A 107 GLY A 122 1 16 HELIX 8 AA8 THR A 124 GLY A 140 1 17 HELIX 9 AA9 SER A 142 GLY A 157 1 16 HELIX 10 AB1 THR A 159 GLY A 175 1 17 HELIX 11 AB2 SER A 177 GLY A 192 1 16 HELIX 12 AB3 THR A 194 LEU A 209 1 16 LINK NE2 HIS A 148 FE HEM A 302 1555 1555 2.05 LINK N1 IMD A 301 FE HEM A 302 1555 1555 1.92 CRYST1 51.752 65.159 70.204 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 0.019323 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014244 0.00000