HEADER DE NOVO PROTEIN 22-JAN-25 9I38 TITLE SOLUTION STRUCTURE OF THE DE NOVO DESIGNED MONOHEME PROTEIN M4D2 WITH TITLE 2 BOUND IRON(III) 2,4-DIMETHYLDEUTEROPORPHYRIN IX COMPND MOL_ID: 1; COMPND 2 MOLECULE: M4D2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DE NOVO DESIGNED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TEST ORGANISM; SOURCE 3 ORGANISM_TAXID: 457483; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: T7 EXPRESS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PET; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: 151 KEYWDS HEME, COFACTOR BINDING, DE NOVO DESIGNED, REDOX PROTEIN, DE NOVO KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.WILLIAMS,G.H.HUTCHINS,P.M.MOLINARO,J.C.BERRONES-REYES, AUTHOR 2 B.R.LICHTENSTEIN,R.L.KODER,J.L.R.ANDERSON REVDAT 1 04-FEB-26 9I38 0 JRNL AUTH C.WILLIAMS,G.H.HUTCHINS,P.M.MOLINARO,J.C.BERRONES-REYES, JRNL AUTH 2 B.R.LICHTENSTEIN,R.L.KODER,J.L.R.ANDERSON JRNL TITL SOLUTION STRUCTURE OF THE DE NOVO DESIGNED MONOHEME PROTEIN JRNL TITL 2 M4D2 WITH BOUND IRON(III) 2,4-DIMETHYLDEUTEROPORPHYRIN IX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.21, ARIA 2.3.2 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), LINGE, O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CNS RUN THROUGH ARIA 2.3.2 REMARK 4 REMARK 4 9I38 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1292142156. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 308; 308; 298 REMARK 210 PH : 6.4; 6.4; 6.4; 6.4 REMARK 210 IONIC STRENGTH : 50; 50; 50; 50 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-15N] M4D2, 1 MM FE(III) REMARK 210 2,4-DIMETHYL DEUTEROPORPHYRIN IX, REMARK 210 20 MM POTASSIUM PHOSPHATE, 50 REMARK 210 MM POTASSIUM CHLORIDE, 90% H2O/ REMARK 210 10% D2O; 1 MM [U-100% 13C; U-100% REMARK 210 15N] M4D2, 1 MM FE(III) 2,4- REMARK 210 DIMETHYL DEUTEROPORPHYRIN IX, 20 REMARK 210 NM POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 2D 1H-13C HSQC; 3D HN(CO)CA; 3D REMARK 210 HNCA; 3D HNCACB; 3D HNCO; 3D 1H- REMARK 210 13C NOESY; 3D H(CCO)NH; 3D REMARK 210 HNCACO; 3D HCCH-TOCSY; 3D REMARK 210 CBCA(CO)NH; 3D 1H-15N TOCSY; 3D REMARK 210 CC(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS 2.4.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 SER A 28 60.38 -156.94 REMARK 500 1 SER A 58 136.81 -171.90 REMARK 500 1 ASN A 87 105.56 63.77 REMARK 500 2 SER A 28 75.86 62.62 REMARK 500 2 PRO A 59 40.03 -79.10 REMARK 500 2 ASN A 87 82.25 54.23 REMARK 500 2 LYS A 111 72.10 49.57 REMARK 500 3 LYS A 111 48.69 -105.10 REMARK 500 4 SER A 2 86.46 -173.19 REMARK 500 4 PRO A 59 35.17 -80.77 REMARK 500 4 SER A 86 50.45 -99.23 REMARK 500 5 THR A 27 43.08 -86.07 REMARK 500 5 SER A 28 39.74 -87.62 REMARK 500 5 ASN A 29 71.16 52.16 REMARK 500 6 SER A 2 56.70 -155.22 REMARK 500 6 SER A 56 48.68 -76.86 REMARK 500 6 PRO A 59 47.72 -77.84 REMARK 500 6 SER A 60 109.30 -167.08 REMARK 500 7 SER A 2 56.61 -143.63 REMARK 500 7 SER A 86 63.10 -107.17 REMARK 500 8 LYS A 111 46.12 -98.19 REMARK 500 9 ASN A 26 -36.85 72.87 REMARK 500 9 SER A 28 44.69 -102.87 REMARK 500 9 SER A 58 136.81 -171.13 REMARK 500 9 SER A 86 43.68 -82.40 REMARK 500 9 SER A 88 132.19 174.90 REMARK 500 9 LYS A 111 35.53 -98.97 REMARK 500 10 ASN A 29 69.75 -118.32 REMARK 500 10 VAL A 57 -62.09 69.71 REMARK 500 10 PRO A 59 46.63 -79.48 REMARK 500 11 SER A 2 50.98 -148.45 REMARK 500 11 SER A 28 49.28 -76.20 REMARK 500 12 SER A 2 54.99 -153.02 REMARK 500 12 THR A 27 96.64 -44.32 REMARK 500 12 SER A 28 30.22 -147.93 REMARK 500 12 SER A 86 17.80 -150.66 REMARK 500 12 ASN A 87 56.83 -111.56 REMARK 500 12 SER A 88 74.48 -159.81 REMARK 500 13 SER A 58 146.26 -172.68 REMARK 500 14 THR A 27 43.80 -82.77 REMARK 500 14 SER A 58 76.78 57.36 REMARK 500 14 ASN A 87 88.24 -69.38 REMARK 500 15 SER A 28 52.17 -140.08 REMARK 500 15 SER A 86 15.83 58.95 REMARK 500 15 LYS A 111 50.28 -105.29 REMARK 500 16 ASN A 29 88.24 -66.56 REMARK 500 16 PRO A 59 40.36 -81.57 REMARK 500 16 SER A 60 116.87 -166.79 REMARK 500 16 SER A 86 19.79 58.29 REMARK 500 17 SER A 2 86.97 61.81 REMARK 500 REMARK 500 THIS ENTRY HAS 64 RAMACHANDRAN OUTLIERS. 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 FDD A 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 37 NE2 REMARK 620 2 FDD A 200 ND 90.2 REMARK 620 3 FDD A 200 NA 89.9 90.0 REMARK 620 4 FDD A 200 NC 90.2 90.1 179.8 REMARK 620 5 FDD A 200 NB 90.4 179.4 89.9 90.0 REMARK 620 6 HIS A 95 NE2 179.1 89.4 90.8 89.0 90.0 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7AH0 RELATED DB: PDB REMARK 900 7AH0 SERVES AS A DESIGN TEMPLATE WITH ONE IDENTICAL HEME BINDING REMARK 900 SITE TO THIS PROTEIN REMARK 900 RELATED ID: 34977 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE DE NOVO DESIGNED MONOHEME PROTEIN M4D2 REMARK 900 WITH BOUND IRON(III) 2,4-DIMETHYLDEUTEROPORPHYRIN IX DBREF 9I38 A 1 112 PDB 9I38 9I38 1 112 SEQRES 1 A 112 GLY SER PRO GLU LEU ARG GLU LYS LEU ARG ALA LEU ILE SEQRES 2 A 112 GLU GLN VAL TYR ALA THR GLY GLN GLU MET LEU LYS ASN SEQRES 3 A 112 THR SER ASN SER PRO GLU LEU ARG GLU LYS HIS ARG ALA SEQRES 4 A 112 LEU ALA GLU GLN VAL TYR ALA THR TRP GLN GLU LEU LEU SEQRES 5 A 112 LYS ASN GLY SER VAL SER PRO SER PRO GLU LEU ARG GLU SEQRES 6 A 112 LYS PHE ARG ALA LEU LEU GLU GLN VAL TYR ALA THR GLY SEQRES 7 A 112 GLN GLU MET LEU LYS ASN THR SER ASN SER PRO GLU LEU SEQRES 8 A 112 ARG GLU LYS HIS ARG ALA LEU ALA GLU GLN VAL ILE ALA SEQRES 9 A 112 THR TRP GLN GLU LEU LEU LYS ASN HET FDD A 200 71 HETNAM FDD FE(III) 2,4-DIMETHYL DEUTEROPORPHYRIN IX FORMUL 2 FDD C32 H32 FE N4 O4 5+ HELIX 1 AA1 SER A 2 LYS A 25 1 24 HELIX 2 AA2 SER A 30 GLY A 55 1 26 HELIX 3 AA3 SER A 60 LYS A 83 1 24 HELIX 4 AA4 SER A 88 LYS A 111 1 24 LINK NE2 HIS A 37 FE FDD A 200 1555 1555 1.97 LINK NE2 HIS A 95 FE FDD A 200 1555 1555 1.97 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL CONECT 593 1842 CONECT 1530 1842 CONECT 1824 1825 CONECT 1825 1824 1826 1827 CONECT 1826 1825 CONECT 1827 1825 1828 1865 1866 CONECT 1828 1827 1829 1867 1868 CONECT 1829 1828 1830 1832 CONECT 1830 1829 1831 1835 CONECT 1831 1830 1869 1870 1871 CONECT 1832 1829 1833 1834 CONECT 1833 1832 1844 1872 CONECT 1834 1832 1835 1842 CONECT 1835 1830 1834 1836 CONECT 1836 1835 1837 1873 CONECT 1837 1836 1838 1845 CONECT 1838 1837 1839 1840 CONECT 1839 1838 1874 1875 1876 CONECT 1840 1838 1841 1846 CONECT 1841 1840 1877 1878 1879 CONECT 1842 593 1530 1834 1843 CONECT 1842 1845 1853 CONECT 1843 1842 1844 1856 CONECT 1844 1833 1843 1859 CONECT 1845 1837 1842 1846 CONECT 1846 1840 1845 1847 CONECT 1847 1846 1848 1880 CONECT 1848 1847 1849 1853 CONECT 1849 1848 1850 1851 CONECT 1850 1849 1881 1882 1883 CONECT 1851 1849 1852 1854 CONECT 1852 1851 1884 1885 1886 CONECT 1853 1842 1848 1854 CONECT 1854 1851 1853 1855 CONECT 1855 1854 1856 1887 CONECT 1856 1843 1855 1857 CONECT 1857 1856 1858 1859 CONECT 1858 1857 1888 1889 1890 CONECT 1859 1844 1857 1860 CONECT 1860 1859 1861 1891 1892 CONECT 1861 1860 1862 1893 1894 CONECT 1862 1861 1863 1864 CONECT 1863 1862 CONECT 1864 1862 CONECT 1865 1827 CONECT 1866 1827 CONECT 1867 1828 CONECT 1868 1828 CONECT 1869 1831 CONECT 1870 1831 CONECT 1871 1831 CONECT 1872 1833 CONECT 1873 1836 CONECT 1874 1839 CONECT 1875 1839 CONECT 1876 1839 CONECT 1877 1841 CONECT 1878 1841 CONECT 1879 1841 CONECT 1880 1847 CONECT 1881 1850 CONECT 1882 1850 CONECT 1883 1850 CONECT 1884 1852 CONECT 1885 1852 CONECT 1886 1852 CONECT 1887 1855 CONECT 1888 1858 CONECT 1889 1858 CONECT 1890 1858 CONECT 1891 1860 CONECT 1892 1860 CONECT 1893 1861 CONECT 1894 1861 MASTER 183 0 1 4 0 0 0 6 947 1 74 9 END