HEADER OXIDOREDUCTASE 03-DEC-19 6TM3 TITLE STRUCTURE OF METHYLENE-TETRAHYDROMETHANOPTERIN DEHYDROGENASE FROM TITLE 2 METHYLORUBRUM EXTORQUENS AM1 IN A CLOSE CONFORMATION CONTAINING NADP+ TITLE 3 AND METHYLENE-H4MPT COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL PROTEIN MDTA; COMPND 3 CHAIN: A; COMPND 4 EC: 1.5.1.-,1.5.1.5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLORUBRUM EXTORQUENS AM1; SOURCE 3 ORGANISM_TAXID: 272630; SOURCE 4 GENE: MTDA, MEXAM1_META1P1728; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-24B(+) KEYWDS ONE-CARBON METABOLISM; ENZYME CATALYSIS; DEHYDROGENASE; KEYWDS 2 CONFORMATIONAL CHANGES; METHYLOTROPHY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.WAGNER,G.HUANG,U.DEMMER,E.WARKENTIN,U.ERMLER,S.SHIMA REVDAT 3 24-JAN-24 6TM3 1 LINK REVDAT 2 20-MAY-20 6TM3 1 JRNL REVDAT 1 26-FEB-20 6TM3 0 JRNL AUTH G.HUANG,T.WAGNER,U.DEMMER,E.WARKENTIN,U.ERMLER,S.SHIMA JRNL TITL THE HYDRIDE TRANSFER PROCESS IN NADP-DEPENDENT JRNL TITL 2 METHYLENE-TETRAHYDROMETHANOPTERIN DEHYDROGENASE. JRNL REF J.MOL.BIOL. V. 432 2042 2020 JRNL REFN ESSN 1089-8638 JRNL PMID 32061937 JRNL DOI 10.1016/J.JMB.2020.01.042 REMARK 2 REMARK 2 RESOLUTION. 1.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 143278 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.114 REMARK 3 R VALUE (WORKING SET) : 0.113 REMARK 3 FREE R VALUE : 0.127 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7168 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 41.9180 - 3.3553 1.00 4961 271 0.1263 0.1381 REMARK 3 2 3.3553 - 2.6633 1.00 4735 260 0.1085 0.1130 REMARK 3 3 2.6633 - 2.3267 1.00 4630 278 0.0957 0.1064 REMARK 3 4 2.3267 - 2.1140 1.00 4666 214 0.0881 0.0951 REMARK 3 5 2.1140 - 1.9624 1.00 4648 219 0.0882 0.1110 REMARK 3 6 1.9624 - 1.8467 1.00 4561 266 0.0840 0.0951 REMARK 3 7 1.8467 - 1.7542 1.00 4578 262 0.0794 0.0993 REMARK 3 8 1.7542 - 1.6779 1.00 4572 230 0.0763 0.0861 REMARK 3 9 1.6779 - 1.6133 1.00 4592 241 0.0743 0.0857 REMARK 3 10 1.6133 - 1.5576 1.00 4576 225 0.0725 0.0985 REMARK 3 11 1.5576 - 1.5089 1.00 4545 234 0.0735 0.0942 REMARK 3 12 1.5089 - 1.4658 1.00 4553 224 0.0815 0.1028 REMARK 3 13 1.4658 - 1.4272 1.00 4558 235 0.0881 0.1123 REMARK 3 14 1.4272 - 1.3924 1.00 4557 241 0.0953 0.1286 REMARK 3 15 1.3924 - 1.3607 1.00 4554 220 0.1044 0.1309 REMARK 3 16 1.3607 - 1.3317 1.00 4534 239 0.1073 0.1268 REMARK 3 17 1.3317 - 1.3051 1.00 4546 211 0.1152 0.1255 REMARK 3 18 1.3051 - 1.2805 1.00 4500 249 0.1237 0.1544 REMARK 3 19 1.2805 - 1.2576 1.00 4519 235 0.1405 0.1540 REMARK 3 20 1.2576 - 1.2363 1.00 4517 254 0.1482 0.1696 REMARK 3 21 1.2363 - 1.2163 1.00 4484 235 0.1603 0.1755 REMARK 3 22 1.2163 - 1.1976 1.00 4542 231 0.1744 0.1847 REMARK 3 23 1.1976 - 1.1800 1.00 4531 234 0.1877 0.2062 REMARK 3 24 1.1800 - 1.1634 1.00 4517 216 0.2011 0.2248 REMARK 3 25 1.1634 - 1.1477 1.00 4483 265 0.2288 0.2381 REMARK 3 26 1.1477 - 1.1328 1.00 4440 249 0.2535 0.2625 REMARK 3 27 1.1328 - 1.1186 1.00 4539 243 0.2724 0.2932 REMARK 3 28 1.1186 - 1.1051 0.99 4462 220 0.3035 0.3391 REMARK 3 29 1.1051 - 1.0923 0.95 4262 244 0.3359 0.3359 REMARK 3 30 1.0923 - 1.0800 0.88 3948 223 0.3920 0.4274 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.07 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6TM3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1292105443. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : / REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 143688 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.080 REMARK 200 RESOLUTION RANGE LOW (A) : 88.922 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : 25.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 1.40300 REMARK 200 R SYM FOR SHELL (I) : 1.40300 REMARK 200 FOR SHELL : 0.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1LU9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE CRYSTALLIZED SAMPLE WAS 25 MG/ML REMARK 280 MTDA SUPPLEMENTED WITH 2.5 MM METHENYL-H4MPT, 2 MM NADPH IN 25 REMARK 280 MM TRIS/HCL PH 7.5, 150 MM NACL, 5% GLYCEROL AND 2 MM REMARK 280 DITHIOTHREITOL. 0.7 UL PROTEIN SAMPLE WAS MIXED WITH 0.7 UL OF REMARK 280 THE RESERVOIR SOLUTION CONTAINING 30% W/V POLYETHYLENE GLYCOL REMARK 280 MONOMETHYL ETHER 5000, 100 MM TRIS PH 8.0 AND 200 MM LITHIUM REMARK 280 SULFATE., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 281.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 3 2 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 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 Y+3/4,X+1/4,-Z+1/4 REMARK 290 14555 -Y+3/4,-X+3/4,-Z+3/4 REMARK 290 15555 Y+1/4,-X+1/4,Z+3/4 REMARK 290 16555 -Y+1/4,X+3/4,Z+1/4 REMARK 290 17555 X+3/4,Z+1/4,-Y+1/4 REMARK 290 18555 -X+1/4,Z+3/4,Y+1/4 REMARK 290 19555 -X+3/4,-Z+3/4,-Y+3/4 REMARK 290 20555 X+1/4,-Z+1/4,Y+3/4 REMARK 290 21555 Z+3/4,Y+1/4,-X+1/4 REMARK 290 22555 Z+1/4,-Y+1/4,X+3/4 REMARK 290 23555 -Z+1/4,Y+3/4,X+1/4 REMARK 290 24555 -Z+3/4,-Y+3/4,-X+3/4 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 62.87700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.87700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 62.87700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.87700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 62.87700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 62.87700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 62.87700 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 62.87700 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 62.87700 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 62.87700 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 62.87700 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 62.87700 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 62.87700 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 62.87700 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 62.87700 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 62.87700 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 62.87700 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 62.87700 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 94.31550 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 31.43850 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 31.43850 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 94.31550 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 94.31550 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 94.31550 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 31.43850 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 31.43850 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 94.31550 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 31.43850 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 94.31550 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 31.43850 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 94.31550 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 31.43850 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 31.43850 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 31.43850 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 94.31550 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 31.43850 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 94.31550 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 94.31550 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 94.31550 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 31.43850 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 31.43850 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 94.31550 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 94.31550 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 31.43850 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 31.43850 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 31.43850 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 31.43850 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 94.31550 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 31.43850 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 94.31550 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 31.43850 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 94.31550 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 94.31550 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 94.31550 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 20300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 26.0 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 350 BIOMT1 2 0.000000 0.000000 1.000000 -62.87700 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 62.87700 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 125.75400 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 62.87700 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 125.75400 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 62.87700 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 696 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 795 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 823 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 871 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 891 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 927 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 962 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 978 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 979 LIES ON A SPECIAL POSITION. 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 LYS A 291 REMARK 465 LEU A 292 REMARK 465 ALA A 293 REMARK 465 ALA A 294 REMARK 465 ALA A 295 REMARK 465 LEU A 296 REMARK 465 GLU A 297 REMARK 465 HIS A 298 REMARK 465 HIS A 299 REMARK 465 HIS A 300 REMARK 465 HIS A 301 REMARK 465 HIS A 302 REMARK 465 HIS A 303 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 ASP A 95 49.03 -155.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 987 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A 988 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A 989 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 990 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH A 991 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A 992 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH A 993 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH A 994 DISTANCE = 6.63 ANGSTROMS REMARK 525 HOH A 995 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH A 996 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH A 997 DISTANCE = 6.82 ANGSTROMS REMARK 525 HOH A 998 DISTANCE = 6.86 ANGSTROMS REMARK 525 HOH A 999 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH A1000 DISTANCE = 9.49 ANGSTROMS REMARK 525 HOH A1001 DISTANCE = 10.44 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 H4M A 403 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 LI A 418 LI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 155 OD1 REMARK 620 2 GLN A 158 OE1 112.0 REMARK 620 3 HOH A 610 O 107.1 111.1 REMARK 620 4 HOH A 788 O 108.2 107.2 111.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 LI A 419 LI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 180 OD1 REMARK 620 2 LEU A 203 O 135.0 REMARK 620 3 HOH A 639 O 106.6 106.6 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue H4M A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LI A 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LI A 419 DBREF 6TM3 A 1 288 UNP P55818 MTDA_METEA 1 288 SEQADV 6TM3 VAL A 289 UNP P55818 EXPRESSION TAG SEQADV 6TM3 ASP A 290 UNP P55818 EXPRESSION TAG SEQADV 6TM3 LYS A 291 UNP P55818 EXPRESSION TAG SEQADV 6TM3 LEU A 292 UNP P55818 EXPRESSION TAG SEQADV 6TM3 ALA A 293 UNP P55818 EXPRESSION TAG SEQADV 6TM3 ALA A 294 UNP P55818 EXPRESSION TAG SEQADV 6TM3 ALA A 295 UNP P55818 EXPRESSION TAG SEQADV 6TM3 LEU A 296 UNP P55818 EXPRESSION TAG SEQADV 6TM3 GLU A 297 UNP P55818 EXPRESSION TAG SEQADV 6TM3 HIS A 298 UNP P55818 EXPRESSION TAG SEQADV 6TM3 HIS A 299 UNP P55818 EXPRESSION TAG SEQADV 6TM3 HIS A 300 UNP P55818 EXPRESSION TAG SEQADV 6TM3 HIS A 301 UNP P55818 EXPRESSION TAG SEQADV 6TM3 HIS A 302 UNP P55818 EXPRESSION TAG SEQADV 6TM3 HIS A 303 UNP P55818 EXPRESSION TAG SEQRES 1 A 303 MET SER LYS LYS LEU LEU PHE GLN PHE ASP THR ASP ALA SEQRES 2 A 303 THR PRO SER VAL PHE ASP VAL VAL VAL GLY TYR ASP GLY SEQRES 3 A 303 GLY ALA ASP HIS ILE THR GLY TYR GLY ASN VAL THR PRO SEQRES 4 A 303 ASP ASN VAL GLY ALA TYR VAL ASP GLY THR ILE TYR THR SEQRES 5 A 303 ARG GLY GLY LYS GLU LYS GLN SER THR ALA ILE PHE VAL SEQRES 6 A 303 GLY GLY GLY ASP MET ALA ALA GLY GLU ARG VAL PHE GLU SEQRES 7 A 303 ALA VAL LYS LYS ARG PHE PHE GLY PRO PHE ARG VAL SER SEQRES 8 A 303 CYS MET LEU ASP SER ASN GLY SER ASN THR THR ALA ALA SEQRES 9 A 303 ALA GLY VAL ALA LEU VAL VAL LYS ALA ALA GLY GLY SER SEQRES 10 A 303 VAL LYS GLY LYS LYS ALA VAL VAL LEU ALA GLY THR GLY SEQRES 11 A 303 PRO VAL GLY MET ARG SER ALA ALA LEU LEU ALA GLY GLU SEQRES 12 A 303 GLY ALA GLU VAL VAL LEU CYS GLY ARG LYS LEU ASP LYS SEQRES 13 A 303 ALA GLN ALA ALA ALA ASP SER VAL ASN LYS ARG PHE LYS SEQRES 14 A 303 VAL ASN VAL THR ALA ALA GLU THR ALA ASP ASP ALA SER SEQRES 15 A 303 ARG ALA GLU ALA VAL LYS GLY ALA HIS PHE VAL PHE THR SEQRES 16 A 303 ALA GLY ALA ILE GLY LEU GLU LEU LEU PRO GLN ALA ALA SEQRES 17 A 303 TRP GLN ASN GLU SER SER ILE GLU ILE VAL ALA ASP TYR SEQRES 18 A 303 ASN ALA GLN PRO PRO LEU GLY ILE GLY GLY ILE ASP ALA SEQRES 19 A 303 THR ASP LYS GLY LYS GLU TYR GLY GLY LYS ARG ALA PHE SEQRES 20 A 303 GLY ALA LEU GLY ILE GLY GLY LEU LYS LEU LYS LEU HIS SEQRES 21 A 303 ARG ALA CYS ILE ALA LYS LEU PHE GLU SER SER GLU GLY SEQRES 22 A 303 VAL PHE ASP ALA GLU GLU ILE TYR LYS LEU ALA LYS GLU SEQRES 23 A 303 MET ALA VAL ASP LYS LEU ALA ALA ALA LEU GLU HIS HIS SEQRES 24 A 303 HIS HIS HIS HIS HET NAP A 401 48 HET GOL A 402 6 HET H4M A 403 31 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HET EDO A 408 4 HET EDO A 409 4 HET EDO A 410 4 HET EDO A 411 4 HET EDO A 412 4 HET EDO A 413 4 HET EDO A 414 4 HET EDO A 415 4 HET EDO A 416 4 HET EDO A 417 4 HET LI A 418 1 HET LI A 419 1 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM GOL GLYCEROL HETNAM H4M 5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN HETNAM EDO 1,2-ETHANEDIOL HETNAM LI LITHIUM ION HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 GOL C3 H8 O3 FORMUL 4 H4M C31 H45 N6 O16 P FORMUL 5 EDO 14(C2 H6 O2) FORMUL 19 LI 2(LI 1+) FORMUL 21 HOH *501(H2 O) HELIX 1 AA1 SER A 16 GLY A 26 1 11 HELIX 2 AA2 ASN A 41 TYR A 51 1 11 HELIX 3 AA3 GLY A 54 GLN A 59 5 6 HELIX 4 AA4 ASP A 69 PHE A 84 1 16 HELIX 5 AA5 GLY A 98 ALA A 114 1 17 HELIX 6 AA6 GLY A 130 GLU A 143 1 14 HELIX 7 AA7 LYS A 153 LYS A 169 1 17 HELIX 8 AA8 ASP A 179 VAL A 187 1 9 HELIX 9 AA9 PRO A 205 TRP A 209 5 5 HELIX 10 AB1 GLY A 248 PHE A 268 1 21 HELIX 11 AB2 ASP A 276 ASP A 290 1 15 SHEET 1 AA1 5 HIS A 30 TYR A 34 0 SHEET 2 AA1 5 LEU A 5 ASP A 10 1 N ASP A 10 O TYR A 34 SHEET 3 AA1 5 THR A 61 GLY A 66 1 O PHE A 64 N PHE A 9 SHEET 4 AA1 5 SER A 91 LEU A 94 1 O MET A 93 N VAL A 65 SHEET 5 AA1 5 VAL A 274 PHE A 275 1 O PHE A 275 N CYS A 92 SHEET 1 AA2 7 THR A 173 GLU A 176 0 SHEET 2 AA2 7 GLU A 146 GLY A 151 1 N LEU A 149 O THR A 173 SHEET 3 AA2 7 LYS A 122 LEU A 126 1 N ALA A 123 O GLU A 146 SHEET 4 AA2 7 PHE A 192 THR A 195 1 O PHE A 194 N LEU A 126 SHEET 5 AA2 7 ILE A 217 ASP A 220 1 O ALA A 219 N THR A 195 SHEET 6 AA2 7 LYS A 244 PHE A 247 1 O PHE A 247 N ASP A 220 SHEET 7 AA2 7 LYS A 237 TYR A 241 -1 N TYR A 241 O LYS A 244 LINK OD1 ASP A 155 LI LI A 418 1555 1555 1.94 LINK OE1 GLN A 158 LI LI A 418 1555 1555 1.87 LINK OD1 ASP A 180 LI LI A 419 1555 1555 2.00 LINK O LEU A 203 LI LI A 419 1555 1555 2.25 LINK LI LI A 418 O HOH A 610 1555 16545 1.98 LINK LI LI A 418 O HOH A 788 1555 1555 1.89 LINK LI LI A 419 O HOH A 639 1555 1555 2.29 CISPEP 1 PRO A 225 PRO A 226 0 -3.70 SITE 1 AC1 35 ASN A 97 THR A 102 ALA A 127 THR A 129 SITE 2 AC1 35 GLY A 130 PRO A 131 VAL A 132 GLY A 151 SITE 3 AC1 35 ARG A 152 LYS A 156 ALA A 196 GLY A 197 SITE 4 AC1 35 ALA A 198 ILE A 199 LEU A 201 TYR A 221 SITE 5 AC1 35 ALA A 249 GLY A 253 LYS A 256 H4M A 403 SITE 6 AC1 35 HOH A 531 HOH A 559 HOH A 579 HOH A 590 SITE 7 AC1 35 HOH A 596 HOH A 599 HOH A 601 HOH A 632 SITE 8 AC1 35 HOH A 645 HOH A 665 HOH A 690 HOH A 704 SITE 9 AC1 35 HOH A 732 HOH A 755 HOH A 802 SITE 1 AC2 13 GLN A 158 ASP A 162 ASN A 165 VAL A 172 SITE 2 AC2 13 EDO A 415 HOH A 510 HOH A 522 HOH A 535 SITE 3 AC2 13 HOH A 614 HOH A 643 HOH A 767 HOH A 809 SITE 4 AC2 13 HOH A 838 SITE 1 AC3 19 SER A 16 PHE A 18 ASP A 19 TYR A 51 SITE 2 AC3 19 THR A 52 ARG A 53 GLY A 54 ASN A 97 SITE 3 AC3 19 GLY A 98 LEU A 250 GLY A 253 LYS A 256 SITE 4 AC3 19 LEU A 257 NAP A 401 EDO A 404 HOH A 505 SITE 5 AC3 19 HOH A 577 HOH A 668 HOH A 977 SITE 1 AC4 8 SER A 16 H4M A 403 HOH A 583 HOH A 603 SITE 2 AC4 8 HOH A 850 HOH A 934 HOH A 970 HOH A 977 SITE 1 AC5 5 LEU A 139 GLU A 278 HOH A 501 HOH A 582 SITE 2 AC5 5 HOH A 604 SITE 1 AC6 5 GLY A 68 HOH A 560 HOH A 579 HOH A 600 SITE 2 AC6 5 HOH A 719 SITE 1 AC7 7 GLU A 279 LYS A 282 LEU A 283 EDO A 417 SITE 2 AC7 7 HOH A 594 HOH A 649 HOH A 718 SITE 1 AC8 4 GLY A 242 GLY A 243 LYS A 244 HOH A 520 SITE 1 AC9 6 PHE A 85 LYS A 166 PRO A 225 HOH A 578 SITE 2 AC9 6 HOH A 653 HOH A 862 SITE 1 AD1 8 PRO A 39 ASP A 40 LYS A 82 EDO A 416 SITE 2 AD1 8 HOH A 533 HOH A 543 HOH A 672 HOH A 745 SITE 1 AD2 5 LYS A 3 ASP A 29 HIS A 30 HOH A 606 SITE 2 AD2 5 HOH A 689 SITE 1 AD3 4 ARG A 152 HOH A 710 HOH A 754 HOH A 812 SITE 1 AD4 3 ARG A 83 GLN A 224 HOH A 680 SITE 1 AD5 10 PHE A 85 PHE A 88 ALA A 223 LEU A 227 SITE 2 AD5 10 ALA A 234 LEU A 250 GOL A 402 HOH A 510 SITE 3 AD5 10 HOH A 522 HOH A 911 SITE 1 AD6 7 PRO A 39 ASP A 40 LYS A 82 EDO A 411 SITE 2 AD6 7 HOH A 533 HOH A 543 HOH A 745 SITE 1 AD7 8 GLY A 273 VAL A 274 PHE A 275 GLU A 279 SITE 2 AD7 8 EDO A 407 HOH A 504 HOH A 516 HOH A 674 SITE 1 AD8 4 ASP A 155 GLN A 158 HOH A 610 HOH A 788 SITE 1 AD9 5 ASP A 180 ARG A 183 LEU A 203 PRO A 205 SITE 2 AD9 5 HOH A 639 CRYST1 125.754 125.754 125.754 90.00 90.00 90.00 P 41 3 2 24 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 0.007952 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007952 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007952 0.00000