HEADER ELECTRON TRANSPORT 02-OCT-20 7AKT TITLE CRPETF VARIANT - A39G_A41V COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERREDOXIN, CHLOROPLASTIC; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHLAMYDOMONAS REINHARDTII; SOURCE 3 ORGANISM_TAXID: 3055; SOURCE 4 GENE: PETF; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS FERREDOXIN, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR G.KURISU,Y.OHNISHI,V.ENGELBRECHT,T.HAPPE REVDAT 2 31-JAN-24 7AKT 1 REMARK REVDAT 1 13-OCT-21 7AKT 0 JRNL AUTH V.ENGELBRECHT,A.HEMSCHEMEIER,M.HEGHMANNS,J.THOMSEN,A.RUTZ, JRNL AUTH 2 S.YADAV,Y.OHNISHI,U.-P.APFEL,M.KASANMASCHEFF,G.KURISU, JRNL AUTH 3 T.HAPPE JRNL TITL FERREDOXIN 2.0: AN ELECTRON TRANSFER PROTEIN DESIGNED INTO A JRNL TITL 2 PHOTOSYSTEM I-DRIVEN HYDROGENASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX VERSION 1.14-3260 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.550 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 31103 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3140 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 25.8100 - 3.0885 0.99 1317 152 0.1594 0.1738 REMARK 3 2 3.0885 - 2.4521 1.00 1293 146 0.1712 0.2184 REMARK 3 3 2.4521 - 2.1423 1.00 1292 138 0.1587 0.1664 REMARK 3 4 2.1423 - 1.9465 1.00 1296 146 0.1535 0.1565 REMARK 3 5 1.9465 - 1.8070 1.00 1285 147 0.1536 0.1684 REMARK 3 6 1.8070 - 1.7005 1.00 1276 143 0.1523 0.1829 REMARK 3 7 1.7005 - 1.6153 1.00 1288 142 0.1526 0.1728 REMARK 3 8 1.6153 - 1.5450 0.99 1280 152 0.1542 0.1543 REMARK 3 9 1.5450 - 1.4856 1.00 1280 149 0.1593 0.1783 REMARK 3 10 1.4856 - 1.4343 1.00 1268 135 0.1648 0.1742 REMARK 3 11 1.4343 - 1.3895 1.00 1305 144 0.1842 0.2079 REMARK 3 12 1.3895 - 1.3498 1.00 1275 147 0.1957 0.2037 REMARK 3 13 1.3498 - 1.3142 1.00 1283 140 0.1989 0.2199 REMARK 3 14 1.3142 - 1.2822 1.00 1261 150 0.2013 0.2113 REMARK 3 15 1.2822 - 1.2530 0.99 1295 146 0.1992 0.2044 REMARK 3 16 1.2530 - 1.2263 1.00 1277 139 0.2111 0.2243 REMARK 3 17 1.2263 - 1.2018 1.00 1307 137 0.2267 0.2749 REMARK 3 18 1.2018 - 1.1791 1.00 1226 148 0.2473 0.2583 REMARK 3 19 1.1791 - 1.1581 0.99 1294 152 0.2800 0.2814 REMARK 3 20 1.1581 - 1.1384 1.00 1271 131 0.3476 0.3716 REMARK 3 21 1.1384 - 1.1201 0.99 1269 154 0.4036 0.4036 REMARK 3 22 1.1201 - 1.1100 0.79 1025 102 0.5532 0.5664 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 889 REMARK 3 ANGLE : 1.247 1221 REMARK 3 CHIRALITY : 0.083 133 REMARK 3 PLANARITY : 0.006 167 REMARK 3 DIHEDRAL : 9.806 458 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 7AKT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1292111538. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31128 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.110 REMARK 200 RESOLUTION RANGE LOW (A) : 25.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.380 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.78300 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: PHENIX REMARK 200 STARTING MODEL: 6LK1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 % (W/V) BENZAMIDINE HYDROCHLORIDE, REMARK 280 1.8 M (NH4)2SO4 AND 0.2 M NASCN IN 0.1 M SODIUM CITRATE BUFFER, REMARK 280 PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281.15K 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 25.61550 REMARK 290 SMTRY3 2 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 -14 REMARK 465 ALA A -13 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A -12 OG REMARK 470 GLU A -5 CG CD OE1 OE2 REMARK 470 ILE A -3 CG1 CG2 CD1 REMARK 470 GLU A -2 CG CD OE1 OE2 REMARK 470 ARG A 0 CD NE CZ NH1 NH2 REMARK 470 LYS A 2 CE NZ REMARK 470 GLU A 15 CG CD OE1 OE2 REMARK 470 LYS A 48 CE NZ 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 SER A 36 -65.16 -145.56 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 NA A 104 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 19 OD2 REMARK 620 2 HOH A 205 O 92.5 REMARK 620 3 HOH A 229 O 94.3 82.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 101 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 37 SG REMARK 620 2 FES A 101 S1 117.7 REMARK 620 3 FES A 101 S2 99.9 102.8 REMARK 620 4 CYS A 42 SG 108.1 107.5 121.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 101 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 45 SG REMARK 620 2 FES A 101 S1 112.1 REMARK 620 3 FES A 101 S2 111.9 105.0 REMARK 620 4 CYS A 75 SG 108.5 114.7 104.4 REMARK 620 N 1 2 3 DBREF 7AKT A 1 94 UNP P07839 FER_CHLRE 33 126 SEQADV 7AKT MET A -14 UNP P07839 INITIATING METHIONINE SEQADV 7AKT ALA A -13 UNP P07839 EXPRESSION TAG SEQADV 7AKT SER A -12 UNP P07839 EXPRESSION TAG SEQADV 7AKT TRP A -11 UNP P07839 EXPRESSION TAG SEQADV 7AKT SER A -10 UNP P07839 EXPRESSION TAG SEQADV 7AKT HIS A -9 UNP P07839 EXPRESSION TAG SEQADV 7AKT PRO A -8 UNP P07839 EXPRESSION TAG SEQADV 7AKT GLN A -7 UNP P07839 EXPRESSION TAG SEQADV 7AKT PHE A -6 UNP P07839 EXPRESSION TAG SEQADV 7AKT GLU A -5 UNP P07839 EXPRESSION TAG SEQADV 7AKT LYS A -4 UNP P07839 EXPRESSION TAG SEQADV 7AKT ILE A -3 UNP P07839 EXPRESSION TAG SEQADV 7AKT GLU A -2 UNP P07839 EXPRESSION TAG SEQADV 7AKT GLY A -1 UNP P07839 EXPRESSION TAG SEQADV 7AKT ARG A 0 UNP P07839 EXPRESSION TAG SEQADV 7AKT GLY A 39 UNP P07839 ALA 71 ENGINEERED MUTATION SEQADV 7AKT VAL A 41 UNP P07839 ALA 73 ENGINEERED MUTATION SEQRES 1 A 109 MET ALA SER TRP SER HIS PRO GLN PHE GLU LYS ILE GLU SEQRES 2 A 109 GLY ARG TYR LYS VAL THR LEU LYS THR PRO SER GLY ASP SEQRES 3 A 109 LYS THR ILE GLU CYS PRO ALA ASP THR TYR ILE LEU ASP SEQRES 4 A 109 ALA ALA GLU GLU ALA GLY LEU ASP LEU PRO TYR SER CYS SEQRES 5 A 109 ARG GLY GLY VAL CYS SER SER CYS ALA GLY LYS VAL ALA SEQRES 6 A 109 ALA GLY THR VAL ASP GLN SER ASP GLN SER PHE LEU ASP SEQRES 7 A 109 ASP ALA GLN MET GLY ASN GLY PHE VAL LEU THR CYS VAL SEQRES 8 A 109 ALA TYR PRO THR SER ASP CYS THR ILE GLN THR HIS GLN SEQRES 9 A 109 GLU GLU ALA LEU TYR HET FES A 101 4 HET BEN A 102 9 HET BEN A 103 9 HET NA A 104 1 HET CL A 105 1 HETNAM FES FE2/S2 (INORGANIC) CLUSTER HETNAM BEN BENZAMIDINE HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 2 FES FE2 S2 FORMUL 3 BEN 2(C7 H8 N2) FORMUL 5 NA NA 1+ FORMUL 6 CL CL 1- FORMUL 7 HOH *78(H2 O) HELIX 1 AA1 GLN A -7 GLU A -2 1 6 HELIX 2 AA2 TYR A 21 ALA A 29 1 9 HELIX 3 AA3 ASP A 63 ASN A 69 1 7 HELIX 4 AA4 CYS A 75 ALA A 77 5 3 HELIX 5 AA5 GLN A 89 LEU A 93 5 5 SHEET 1 AA1 5 GLY A 10 CYS A 16 0 SHEET 2 AA1 5 TYR A 1 THR A 7 -1 N VAL A 3 O ILE A 14 SHEET 3 AA1 5 CYS A 83 GLN A 86 1 O CYS A 83 N THR A 4 SHEET 4 AA1 5 ALA A 46 ALA A 51 -1 N LYS A 48 O GLN A 86 SHEET 5 AA1 5 PHE A 71 LEU A 73 -1 O VAL A 72 N GLY A 47 SHEET 1 AA2 2 VAL A 54 ASP A 55 0 SHEET 2 AA2 2 TYR A 78 PRO A 79 -1 O TYR A 78 N ASP A 55 LINK OD2 ASP A 19 NA NA A 104 1555 1555 2.67 LINK SG CYS A 37 FE1 FES A 101 1555 1555 2.32 LINK SG CYS A 42 FE1 FES A 101 1555 1555 2.26 LINK SG CYS A 45 FE2 FES A 101 1555 1555 2.29 LINK SG CYS A 75 FE2 FES A 101 1555 1555 2.29 LINK NA NA A 104 O HOH A 205 1555 1455 2.64 LINK NA NA A 104 O HOH A 229 1555 1455 2.73 CRYST1 25.966 51.231 32.255 90.00 112.13 90.00 P 1 21 1 2 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 0.038512 0.000000 0.015664 0.00000 SCALE2 0.000000 0.019519 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033469 0.00000