HEADER DE NOVO PROTEIN 12-AUG-20 7JRQ TITLE CRYSTALLOGRAPHICALLY CHARACTERIZED DE NOVO DESIGNED MN- TITLE 2 DIPHENYLPORPHYRIN BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MPP1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METALLOPROTEIN, PORPHYRIN, OXIDATION, SULFOXIDATION, HIGH-TALENT, KEYWDS 2 HELICAL BUNDLE, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.I.MANN,W.F.DEGRADO REVDAT 4 18-OCT-23 7JRQ 1 REMARK REVDAT 3 27-JAN-21 7JRQ 1 JRNL REVDAT 2 20-JAN-21 7JRQ 1 JRNL REVDAT 1 13-JAN-21 7JRQ 0 JRNL AUTH S.I.MANN,A.NAYAK,G.T.GASSNER,M.J.THERIEN,W.F.DEGRADO JRNL TITL DE NOVO DESIGN, SOLUTION CHARACTERIZATION, AND JRNL TITL 2 CRYSTALLOGRAPHIC STRUCTURE OF AN ABIOLOGICAL JRNL TITL 3 MN-PORPHYRIN-BINDING PROTEIN CAPABLE OF STABILIZING A MN(V) JRNL TITL 4 SPECIES. JRNL REF J.AM.CHEM.SOC. V. 143 252 2021 JRNL REFN ESSN 1520-5126 JRNL PMID 33373215 JRNL DOI 10.1021/JACS.0C10136 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18_3861 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 18042 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1796 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 39.6800 - 4.1200 1.00 1403 154 0.1930 0.2104 REMARK 3 2 4.1100 - 3.2700 1.00 1305 144 0.1680 0.1949 REMARK 3 3 3.2600 - 2.8500 1.00 1284 141 0.1834 0.2082 REMARK 3 4 2.8500 - 2.5900 1.00 1269 141 0.1856 0.2431 REMARK 3 5 2.5900 - 2.4100 1.00 1247 138 0.1727 0.2385 REMARK 3 6 2.4100 - 2.2600 1.00 1243 137 0.1718 0.2215 REMARK 3 7 2.2600 - 2.1500 0.99 1237 137 0.1755 0.2000 REMARK 3 8 2.1500 - 2.0600 1.00 1228 136 0.1967 0.2789 REMARK 3 9 2.0600 - 1.9800 0.99 1242 137 0.2290 0.2449 REMARK 3 10 1.9800 - 1.9100 0.99 1214 134 0.2361 0.2590 REMARK 3 11 1.9100 - 1.8500 0.99 1239 139 0.2607 0.3212 REMARK 3 12 1.8500 - 1.8000 0.98 1191 133 0.2834 0.2962 REMARK 3 13 1.8000 - 1.7500 0.95 1144 125 0.3259 0.3814 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) : 0.188 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.035 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.08 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 : 0.008 1203 REMARK 3 ANGLE : 0.725 1641 REMARK 3 CHIRALITY : 0.036 158 REMARK 3 PLANARITY : 0.018 214 REMARK 3 DIHEDRAL : 22.484 176 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 7JRQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251292. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .99 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18042 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 39.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 5TGY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 0.8 M NAH2PO4, 0.8 REMARK 280 M KH2PO4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.11000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.66100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.66100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.05500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.66100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.66100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 123.16500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.66100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.66100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.05500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.66100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.66100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 123.16500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 82.11000 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 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 HIS A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 19 CD REMARK 480 GLU A 30 CD REMARK 480 LYS A 63 CD REMARK 480 GLU A 112 CD OE1 OE2 REMARK 480 GLU A 113 CD REMARK 480 GLN A 116 CD OE1 NE2 REMARK 480 LEU A 129 CA CB CG CD1 CD2 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 SMU A 203 MN1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 58 OE1 REMARK 620 2 SMU A 203 N3 93.0 REMARK 620 3 SMU A 203 N4 105.1 84.2 REMARK 620 4 SMU A 203 N2 82.0 92.2 172.2 REMARK 620 5 SMU A 203 N1 98.6 167.2 87.5 94.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SMU A 202 MN1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 64 NE2 REMARK 620 2 SMU A 202 N3 94.4 REMARK 620 3 SMU A 202 N4 94.8 88.0 REMARK 620 4 SMU A 202 N2 94.1 92.7 171.0 REMARK 620 5 SMU A 202 N1 91.8 173.2 88.7 89.6 REMARK 620 6 HOH A 322 O 176.7 87.2 88.2 82.9 86.8 REMARK 620 N 1 2 3 4 5 DBREF 7JRQ A 2 132 PDB 7JRQ 7JRQ 2 132 SEQRES 1 A 131 HIS HIS HIS HIS HIS HIS GLU ASN LEU TYR PHE GLN SER SEQRES 2 A 131 SER GLU LYS GLU GLU LEU PHE GLU LYS LEU LYS GLN THR SEQRES 3 A 131 ALA ASP GLU ALA VAL GLN LEU PHE GLN ARG LEU ARG GLU SEQRES 4 A 131 ILE PHE ASP LYS GLY ASP ASP ASP SER PHE GLU GLN VAL SEQRES 5 A 131 LEU GLU GLU LEU GLU GLU ALA LEU GLN LYS HIS ARG GLN SEQRES 6 A 131 LEU ALA ASP GLN GLY ARG LYS LYS GLY LEU LEU THR SER SEQRES 7 A 131 GLU ALA ALA LYS GLN GLY ASP GLN PHE VAL GLN LEU PHE SEQRES 8 A 131 GLN ARG PHE ARG GLU ALA TRP ASP LYS GLY ASP LYS ASP SEQRES 9 A 131 SER LEU GLU GLN ILE LEU GLU GLU LEU GLU GLN VAL ALA SEQRES 10 A 131 GLN LYS ALA VAL GLU LEU GLY LEU LYS ILE LEU LYS THR SEQRES 11 A 131 GLN HET GOL A 201 6 HET SMU A 202 37 HET SMU A 203 37 HET CL A 204 1 HETNAM GOL GLYCEROL HETNAM SMU [5,15-DIPHENYLPORPHYRINATO(2-)-KAPPA~4~N~21~,N~22~, HETNAM 2 SMU N~23~,N~24~]MANGANESE HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 SMU 2(C32 H20 MN N4 2+) FORMUL 5 CL CL 1- FORMUL 6 HOH *37(H2 O) HELIX 1 AA1 ASN A 9 PHE A 12 5 4 HELIX 2 AA2 GLN A 13 GLY A 45 1 33 HELIX 3 AA3 ASP A 46 LYS A 74 1 29 HELIX 4 AA4 SER A 79 GLY A 102 1 24 HELIX 5 AA5 ASP A 103 LYS A 130 1 28 LINK OE1 GLU A 58 MN1 SMU A 203 1555 1555 2.61 LINK NE2 HIS A 64 MN1 SMU A 202 1555 1555 2.39 LINK MN1 SMU A 202 O HOH A 322 1555 1555 2.62 CRYST1 45.322 45.322 164.220 90.00 90.00 90.00 P 41 21 2 8 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 0.022064 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022064 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006089 0.00000