HEADER OXYGEN TRANSPORT 23-MAY-14 4PNJ TITLE RECOMBINANT SPERM WHALE P6 MYOGLOBIN SOLVED WITH SINGLE PULSE FREE TITLE 2 ELECTRON LASER DATA COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; SOURCE 3 ORGANISM_COMMON: SPERM WHALE; SOURCE 4 ORGANISM_TAXID: 9755; SOURCE 5 GENE: MB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MYOGLOBIN, FEMTOSECOND X-RAY CRYSTALLOGRAPHY, OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.COHEN,A.GONZALEZ,W.LAM,A.LYUBIMOV,N.SAUTER,Y.TSAI, AUTHOR 2 M.UERVIROJNANGKOORN,A.BRUNGER,M.SOLTIS REVDAT 7 27-SEP-23 4PNJ 1 REMARK REVDAT 6 28-NOV-18 4PNJ 1 REMARK REVDAT 5 15-NOV-17 4PNJ 1 REMARK REVDAT 4 18-NOV-15 4PNJ 1 REMARK REVDAT 3 17-DEC-14 4PNJ 1 JRNL REVDAT 2 03-DEC-14 4PNJ 1 JRNL REVDAT 1 05-NOV-14 4PNJ 0 JRNL AUTH A.E.COHEN,S.M.SOLTIS,A.GONZALEZ,L.AGUILA,R.ALONSO-MORI, JRNL AUTH 2 C.O.BARNES,E.L.BAXTER,W.BREHMER,A.S.BREWSTER,A.T.BRUNGER, JRNL AUTH 3 G.CALERO,J.F.CHANG,M.CHOLLET,P.EHRENSBERGER,T.L.ERIKSSON, JRNL AUTH 4 Y.FENG,J.HATTNE,B.HEDMAN,M.HOLLENBECK,J.M.HOLTON,S.KEABLE, JRNL AUTH 5 B.K.KOBILKA,E.G.KOVALEVA,A.C.KRUSE,H.T.LEMKE,G.LIN, JRNL AUTH 6 A.Y.LYUBIMOV,A.MANGLIK,I.I.MATHEWS,S.E.MCPHILLIPS,S.NELSON, JRNL AUTH 7 J.W.PETERS,N.K.SAUTER,C.A.SMITH,J.SONG,H.P.STEVENSON,Y.TSAI, JRNL AUTH 8 M.UERVIROJNANGKOORN,V.VINETSKY,S.WAKATSUKI,W.I.WEIS, JRNL AUTH 9 O.A.ZADVORNYY,O.B.ZELDIN,D.ZHU,K.O.HODGSON JRNL TITL GONIOMETER-BASED FEMTOSECOND CRYSTALLOGRAPHY WITH X-RAY FREE JRNL TITL 2 ELECTRON LASERS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 17122 2014 JRNL REFN ESSN 1091-6490 JRNL PMID 25362050 JRNL DOI 10.1073/PNAS.1418733111 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.150 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 43729 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.910 REMARK 3 FREE R VALUE TEST SET COUNT : 2585 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 39.1212 - 3.5529 1.00 2491 154 0.1491 0.1741 REMARK 3 2 3.5529 - 2.8203 1.00 2415 150 0.1465 0.1817 REMARK 3 3 2.8203 - 2.4639 1.00 2390 154 0.1427 0.1941 REMARK 3 4 2.4639 - 2.2386 1.00 2406 149 0.1323 0.1584 REMARK 3 5 2.2386 - 2.0782 1.00 2401 147 0.1350 0.1464 REMARK 3 6 2.0782 - 1.9557 1.00 2396 156 0.1453 0.1873 REMARK 3 7 1.9557 - 1.8577 1.00 2373 145 0.1531 0.1802 REMARK 3 8 1.8577 - 1.7769 1.00 2376 152 0.1571 0.1803 REMARK 3 9 1.7769 - 1.7085 1.00 2385 147 0.1603 0.1974 REMARK 3 10 1.7085 - 1.6495 1.00 2382 152 0.1615 0.1793 REMARK 3 11 1.6495 - 1.5979 1.00 2360 150 0.1716 0.1970 REMARK 3 12 1.5979 - 1.5522 1.00 2366 147 0.1784 0.1852 REMARK 3 13 1.5522 - 1.5114 1.00 2384 151 0.1982 0.2310 REMARK 3 14 1.5114 - 1.4745 1.00 2392 151 0.2091 0.2431 REMARK 3 15 1.4745 - 1.4410 0.99 2322 148 0.2524 0.2773 REMARK 3 16 1.4410 - 1.4103 0.92 2185 131 0.3065 0.3481 REMARK 3 17 1.4103 - 1.3821 0.76 1810 118 0.3510 0.3713 REMARK 3 18 1.3821 - 1.3600 0.55 1310 83 0.3849 0.3890 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.77 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 : 0.013 1467 REMARK 3 ANGLE : 1.432 2008 REMARK 3 CHIRALITY : 0.087 199 REMARK 3 PLANARITY : 0.008 251 REMARK 3 DIHEDRAL : 15.506 540 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 0 THROUGH 19 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.7653 99.4416 4.5983 REMARK 3 T TENSOR REMARK 3 T11: 0.1539 T22: 0.1647 REMARK 3 T33: 0.1375 T12: 0.0006 REMARK 3 T13: 0.0067 T23: -0.0062 REMARK 3 L TENSOR REMARK 3 L11: 0.0619 L22: 0.0645 REMARK 3 L33: 0.1533 L12: -0.0657 REMARK 3 L13: -0.0046 L23: 0.0089 REMARK 3 S TENSOR REMARK 3 S11: -0.0170 S12: -0.0769 S13: -0.0623 REMARK 3 S21: 0.0894 S22: 0.0590 S23: -0.0405 REMARK 3 S31: 0.0769 S32: 0.1261 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 20 THROUGH 35 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.0256 100.1609 -14.5982 REMARK 3 T TENSOR REMARK 3 T11: 0.1318 T22: 0.1477 REMARK 3 T33: 0.1486 T12: 0.0017 REMARK 3 T13: -0.0022 T23: -0.0115 REMARK 3 L TENSOR REMARK 3 L11: 0.0664 L22: 0.0174 REMARK 3 L33: 0.0840 L12: -0.0134 REMARK 3 L13: -0.0366 L23: 0.0468 REMARK 3 S TENSOR REMARK 3 S11: 0.0418 S12: 0.2233 S13: -0.1183 REMARK 3 S21: 0.1091 S22: 0.0416 S23: -0.0857 REMARK 3 S31: 0.0875 S32: 0.1119 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 36 THROUGH 51 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.5530 102.7245 -21.1408 REMARK 3 T TENSOR REMARK 3 T11: 0.1712 T22: 0.2399 REMARK 3 T33: 0.1569 T12: 0.0147 REMARK 3 T13: -0.0060 T23: -0.0138 REMARK 3 L TENSOR REMARK 3 L11: 0.0952 L22: 0.0897 REMARK 3 L33: 0.1109 L12: -0.0242 REMARK 3 L13: -0.0498 L23: 0.0262 REMARK 3 S TENSOR REMARK 3 S11: 0.0786 S12: 0.1639 S13: 0.0398 REMARK 3 S21: -0.1611 S22: -0.0430 S23: 0.0390 REMARK 3 S31: -0.0124 S32: -0.2563 S33: -0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 52 THROUGH 58 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.0682 103.0289 -23.8537 REMARK 3 T TENSOR REMARK 3 T11: 0.1902 T22: 0.2639 REMARK 3 T33: 0.1410 T12: 0.0321 REMARK 3 T13: 0.0174 T23: 0.0210 REMARK 3 L TENSOR REMARK 3 L11: 0.0187 L22: 0.0211 REMARK 3 L33: 0.0290 L12: 0.0075 REMARK 3 L13: 0.0014 L23: 0.0239 REMARK 3 S TENSOR REMARK 3 S11: 0.1420 S12: 0.0338 S13: -0.1515 REMARK 3 S21: -0.0449 S22: -0.0929 S23: -0.1071 REMARK 3 S31: 0.1298 S32: 0.3565 S33: -0.0002 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 59 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.9148 109.0220 -8.4933 REMARK 3 T TENSOR REMARK 3 T11: 0.1260 T22: 0.1525 REMARK 3 T33: 0.1381 T12: -0.0016 REMARK 3 T13: 0.0049 T23: 0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.1014 L22: 0.0604 REMARK 3 L33: 0.0531 L12: -0.0275 REMARK 3 L13: 0.0756 L23: -0.0173 REMARK 3 S TENSOR REMARK 3 S11: -0.0297 S12: 0.0611 S13: 0.0291 REMARK 3 S21: -0.0412 S22: 0.0260 S23: -0.0167 REMARK 3 S31: 0.0294 S32: 0.0268 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 79 THROUGH 95 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.9419 108.4580 1.8428 REMARK 3 T TENSOR REMARK 3 T11: 0.1442 T22: 0.1535 REMARK 3 T33: 0.1606 T12: 0.0072 REMARK 3 T13: 0.0038 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 0.0772 L22: 0.1493 REMARK 3 L33: 0.0223 L12: -0.0581 REMARK 3 L13: -0.0317 L23: 0.0649 REMARK 3 S TENSOR REMARK 3 S11: -0.0346 S12: -0.0686 S13: 0.0370 REMARK 3 S21: 0.0943 S22: -0.0324 S23: 0.0634 REMARK 3 S31: 0.0510 S32: -0.0840 S33: -0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 96 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.1797 105.5351 -11.1470 REMARK 3 T TENSOR REMARK 3 T11: 0.1990 T22: 0.2487 REMARK 3 T33: 0.2033 T12: 0.0134 REMARK 3 T13: 0.0017 T23: -0.0127 REMARK 3 L TENSOR REMARK 3 L11: 0.0021 L22: 0.0114 REMARK 3 L33: 0.0274 L12: -0.0037 REMARK 3 L13: -0.0086 L23: 0.0139 REMARK 3 S TENSOR REMARK 3 S11: 0.1247 S12: 0.2660 S13: -0.0633 REMARK 3 S21: -0.2843 S22: -0.0109 S23: 0.2580 REMARK 3 S31: -0.1255 S32: -0.3876 S33: -0.0001 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 101 THROUGH 124 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.1958 94.0864 -7.5776 REMARK 3 T TENSOR REMARK 3 T11: 0.1387 T22: 0.1419 REMARK 3 T33: 0.1624 T12: -0.0007 REMARK 3 T13: 0.0079 T23: -0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.0931 L22: 0.0798 REMARK 3 L33: 0.2996 L12: -0.0849 REMARK 3 L13: -0.1296 L23: 0.1089 REMARK 3 S TENSOR REMARK 3 S11: 0.0156 S12: -0.0358 S13: -0.1169 REMARK 3 S21: -0.0192 S22: -0.0326 S23: 0.0297 REMARK 3 S31: 0.0618 S32: -0.0223 S33: 0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 125 THROUGH 153 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.8706 98.0523 1.0034 REMARK 3 T TENSOR REMARK 3 T11: 0.1435 T22: 0.1476 REMARK 3 T33: 0.1830 T12: 0.0099 REMARK 3 T13: 0.0173 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 0.0981 L22: 0.0847 REMARK 3 L33: 0.1414 L12: 0.0303 REMARK 3 L13: -0.1066 L23: 0.0096 REMARK 3 S TENSOR REMARK 3 S11: -0.0494 S12: -0.0905 S13: -0.2354 REMARK 3 S21: 0.1151 S22: 0.0391 S23: 0.2041 REMARK 3 S31: 0.0444 S32: -0.0950 S33: -0.0001 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 4PNJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000201698. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : XPP REMARK 200 X-RAY GENERATOR MODEL : SLAC LCLS BEAMLINE XPP REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.31 REMARK 200 MONOCHROMATOR : NONE (SASE PULSE) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : CS-PAD CXI-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CCTBX.XFEL REMARK 200 DATA SCALING SOFTWARE : CCTBX.XFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43767 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 39.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 25.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.9400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 52.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.57 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: MOLREP 11.0.05 REMARK 200 STARTING MODEL: 1VXA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2 - 2.8M (NH4)2SO4 IN 20MM TRISHCL, REMARK 280 PH 9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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: 2220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -95.0 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 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 S SO4 A 207 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 427 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 429 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 508 LIES ON A SPECIAL POSITION. 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 MET A 0 CG SD CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O4 SO4 A 202 O HOH A 301 2.03 REMARK 500 O HOH A 531 O HOH A 622 2.11 REMARK 500 O HOH A 438 O HOH A 543 2.15 REMARK 500 O HOH A 530 O HOH A 603 2.16 REMARK 500 OE1 GLU A 38 O HOH A 628 2.17 REMARK 500 O HOH A 421 O HOH A 426 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 118 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 118 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES 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 ASP A 20 76.88 -161.79 REMARK 500 LYS A 98 63.86 61.20 REMARK 500 PHE A 123 49.34 -142.96 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 474 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A 508 DISTANCE = 7.84 ANGSTROMS REMARK 525 HOH A 519 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH A 568 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH A 580 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A 582 DISTANCE = 6.91 ANGSTROMS REMARK 525 HOH A 631 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A 638 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A 643 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH A 652 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A 653 DISTANCE = 7.98 ANGSTROMS 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 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 93 NE2 REMARK 620 2 HEM A 201 NA 89.6 REMARK 620 3 HEM A 201 NB 91.4 89.3 REMARK 620 4 HEM A 201 NC 92.3 177.5 89.1 REMARK 620 5 HEM A 201 ND 92.0 91.0 176.6 90.5 REMARK 620 6 HOH A 443 O 178.4 90.6 90.1 87.5 86.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 209 DBREF 4PNJ A 0 153 UNP P02185 MYG_PHYCD 1 154 SEQRES 1 A 154 MET VAL LEU SER GLU GLY GLU TRP GLN LEU VAL LEU HIS SEQRES 2 A 154 VAL TRP ALA LYS VAL GLU ALA ASP VAL ALA GLY HIS GLY SEQRES 3 A 154 GLN ASP ILE LEU ILE ARG LEU PHE LYS SER HIS PRO GLU SEQRES 4 A 154 THR LEU GLU LYS PHE ASP ARG PHE LYS HIS LEU LYS THR SEQRES 5 A 154 GLU ALA GLU MET LYS ALA SER GLU ASP LEU LYS LYS HIS SEQRES 6 A 154 GLY VAL THR VAL LEU THR ALA LEU GLY ALA ILE LEU LYS SEQRES 7 A 154 LYS LYS GLY HIS HIS GLU ALA GLU LEU LYS PRO LEU ALA SEQRES 8 A 154 GLN SER HIS ALA THR LYS HIS LYS ILE PRO ILE LYS TYR SEQRES 9 A 154 LEU GLU PHE ILE SER GLU ALA ILE ILE HIS VAL LEU HIS SEQRES 10 A 154 SER ARG HIS PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY SEQRES 11 A 154 ALA MET ASN LYS ALA LEU GLU LEU PHE ARG LYS ASP ILE SEQRES 12 A 154 ALA ALA LYS TYR LYS GLU LEU GLY TYR GLN GLY HET HEM A 201 73 HET SO4 A 202 5 HET SO4 A 203 5 HET SO4 A 204 5 HET SO4 A 205 5 HET SO4 A 206 5 HET SO4 A 207 5 HET SO4 A 208 5 HET SO4 A 209 5 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM SO4 SULFATE ION HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 SO4 8(O4 S 2-) FORMUL 11 HOH *360(H2 O) HELIX 1 AA1 SER A 3 GLU A 18 1 16 HELIX 2 AA2 ASP A 20 HIS A 36 1 17 HELIX 3 AA3 PRO A 37 PHE A 43 5 7 HELIX 4 AA4 THR A 51 SER A 58 1 8 HELIX 5 AA5 SER A 58 LYS A 78 1 21 HELIX 6 AA6 HIS A 82 LYS A 96 1 15 HELIX 7 AA7 PRO A 100 HIS A 119 1 20 HELIX 8 AA8 GLY A 124 LEU A 149 1 26 LINK NE2 HIS A 93 FE HEM A 201 1555 1555 2.16 LINK FE HEM A 201 O HOH A 443 1555 1555 2.17 SITE 1 AC1 22 THR A 39 LYS A 42 PHE A 43 ARG A 45 SITE 2 AC1 22 HIS A 64 THR A 67 VAL A 68 LEU A 89 SITE 3 AC1 22 SER A 92 HIS A 93 HIS A 97 ILE A 99 SITE 4 AC1 22 TYR A 103 LEU A 104 HOH A 313 HOH A 333 SITE 5 AC1 22 HOH A 387 HOH A 443 HOH A 445 HOH A 450 SITE 6 AC1 22 HOH A 487 HOH A 517 SITE 1 AC2 8 ARG A 31 LYS A 98 HOH A 301 HOH A 302 SITE 2 AC2 8 HOH A 316 HOH A 321 HOH A 324 HOH A 358 SITE 1 AC3 8 ARG A 45 LYS A 63 HIS A 64 THR A 67 SITE 2 AC3 8 HOH A 384 HOH A 487 HOH A 522 HOH A 587 SITE 1 AC4 9 LYS A 87 GLY A 124 ALA A 125 ASP A 126 SITE 2 AC4 9 HOH A 310 HOH A 335 HOH A 357 HOH A 447 SITE 3 AC4 9 HOH A 480 SITE 1 AC5 10 SER A 3 GLU A 4 THR A 51 GLU A 52 SITE 2 AC5 10 ALA A 53 HOH A 304 HOH A 322 HOH A 348 SITE 3 AC5 10 HOH A 367 HOH A 453 SITE 1 AC6 8 SER A 3 GLY A 5 HOH A 453 HOH A 521 SITE 2 AC6 8 HOH A 571 HOH A 618 HOH A 630 HOH A 642 SITE 1 AC7 3 ALA A 15 LYS A 16 HOH A 350 SITE 1 AC8 7 GLN A 26 LYS A 56 GLU A 59 LYS A 62 SITE 2 AC8 7 HOH A 490 HOH A 567 HOH A 644 SITE 1 AC9 8 HIS A 48 LEU A 49 HOH A 307 HOH A 494 SITE 2 AC9 8 HOH A 496 HOH A 525 HOH A 533 HOH A 655 CRYST1 90.309 90.309 45.204 90.00 90.00 120.00 P 6 6 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 0.011073 0.006393 0.000000 0.00000 SCALE2 0.000000 0.012786 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022122 0.00000