HEADER TRANSFERASE 18-JUN-20 7CCX TITLE CRYSTAL STRUCTURE OF THE HOLO FORM OF HUMAN HYDROXYMETHYLBILANE TITLE 2 SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PORPHOBILINOGEN DEAMINASE; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: PBG-D,HYDROXYMETHYLBILANE SYNTHASE,HMBS,PRE-UROPORPHYRINOGEN COMPND 5 SYNTHASE; COMPND 6 EC: 2.5.1.61; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HMBS, PBGD, UPS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PORPHYRIN SYNTHESIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.SATO,M.SUGISHIMA,K.WADA,K.HIRABAYASHI,M.TSUKAGUCHI REVDAT 2 29-NOV-23 7CCX 1 REMARK REVDAT 1 17-MAR-21 7CCX 0 JRNL AUTH H.SATO,M.SUGISHIMA,M.TSUKAGUCHI,T.MASUKO,M.IIJIMA,M.TAKANO, JRNL AUTH 2 Y.OMATA,K.HIRABAYASHI,K.WADA,Y.HISAEDA,K.YAMAMOTO JRNL TITL CRYSTAL STRUCTURES OF HYDROXYMETHYLBILANE SYNTHASE COMPLEXED JRNL TITL 2 WITH A SUBSTRATE ANALOG: A SINGLE SUBSTRATE-BINDING SITE FOR JRNL TITL 3 FOUR CONSECUTIVE CONDENSATION STEPS. JRNL REF BIOCHEM.J. V. 478 1023 2021 JRNL REFN ESSN 1470-8728 JRNL PMID 33600566 JRNL DOI 10.1042/BCJ20200996 REMARK 2 REMARK 2 RESOLUTION. 1.84 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 53344 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.740 REMARK 3 FREE R VALUE TEST SET COUNT : 1994 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 43.1500 - 4.4400 0.97 3861 150 0.1684 0.1888 REMARK 3 2 4.4400 - 3.5200 1.00 3803 148 0.1584 0.1876 REMARK 3 3 3.5200 - 3.0800 1.00 3791 147 0.1829 0.2817 REMARK 3 4 3.0800 - 2.8000 0.99 3695 144 0.2119 0.2634 REMARK 3 5 2.8000 - 2.5900 0.98 3673 143 0.2125 0.3016 REMARK 3 6 2.5900 - 2.4400 0.98 3655 141 0.2098 0.3022 REMARK 3 7 2.4400 - 2.3200 0.98 3666 143 0.2069 0.2732 REMARK 3 8 2.3200 - 2.2200 0.98 3686 143 0.2253 0.2716 REMARK 3 9 2.2200 - 2.1300 0.99 3679 142 0.2111 0.3070 REMARK 3 10 2.1300 - 2.0600 0.99 3692 143 0.2243 0.2906 REMARK 3 11 2.0600 - 2.0000 1.00 3721 145 0.2435 0.3038 REMARK 3 12 2.0000 - 1.9400 0.99 3653 142 0.2602 0.3169 REMARK 3 13 1.9400 - 1.8900 0.96 3543 138 0.2941 0.3717 REMARK 3 14 1.8900 - 1.8400 0.87 3232 125 0.3121 0.3305 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) : 0.232 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.172 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.75 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 : 0.006 4894 REMARK 3 ANGLE : 0.745 6644 REMARK 3 CHIRALITY : 0.051 782 REMARK 3 PLANARITY : 0.005 861 REMARK 3 DIHEDRAL : 5.105 3516 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 18 THROUGH 99 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.2426 -23.0159 -28.6306 REMARK 3 T TENSOR REMARK 3 T11: 0.4159 T22: 0.3435 REMARK 3 T33: 0.2784 T12: 0.0223 REMARK 3 T13: -0.0454 T23: -0.0062 REMARK 3 L TENSOR REMARK 3 L11: 2.7779 L22: 3.0692 REMARK 3 L33: 2.1144 L12: -0.6227 REMARK 3 L13: -0.3261 L23: -0.2513 REMARK 3 S TENSOR REMARK 3 S11: 0.1460 S12: 0.0810 S13: -0.1988 REMARK 3 S21: -0.2447 S22: -0.0699 S23: -0.1968 REMARK 3 S31: 0.3906 S32: 0.1322 S33: -0.0877 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 100 THROUGH 228 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.4756 -5.0741 -13.3738 REMARK 3 T TENSOR REMARK 3 T11: 0.2116 T22: 0.3009 REMARK 3 T33: 0.3009 T12: 0.0059 REMARK 3 T13: -0.0071 T23: 0.0259 REMARK 3 L TENSOR REMARK 3 L11: 0.4951 L22: 3.3396 REMARK 3 L33: 5.6784 L12: -0.0834 REMARK 3 L13: 0.1348 L23: 1.2693 REMARK 3 S TENSOR REMARK 3 S11: -0.0401 S12: -0.0381 S13: 0.0706 REMARK 3 S21: 0.1169 S22: 0.0334 S23: 0.0377 REMARK 3 S31: -0.1756 S32: 0.0739 S33: -0.0011 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 229 THROUGH 354 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.0063 -3.0487 -33.2756 REMARK 3 T TENSOR REMARK 3 T11: 0.2700 T22: 0.2911 REMARK 3 T33: 0.2027 T12: -0.0173 REMARK 3 T13: -0.0511 T23: 0.0331 REMARK 3 L TENSOR REMARK 3 L11: 1.0575 L22: 6.5096 REMARK 3 L33: 2.1650 L12: -1.0918 REMARK 3 L13: -0.2421 L23: 0.7128 REMARK 3 S TENSOR REMARK 3 S11: 0.1091 S12: 0.0981 S13: -0.0335 REMARK 3 S21: -0.1987 S22: -0.0829 S23: 0.1115 REMARK 3 S31: 0.1120 S32: -0.0758 S33: -0.0334 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 18 THROUGH 45 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.4331 -25.5759 -5.9371 REMARK 3 T TENSOR REMARK 3 T11: 0.2003 T22: 0.3307 REMARK 3 T33: 0.3271 T12: -0.0297 REMARK 3 T13: -0.0298 T23: 0.0409 REMARK 3 L TENSOR REMARK 3 L11: 5.3950 L22: 7.5051 REMARK 3 L33: 7.5143 L12: 1.2731 REMARK 3 L13: 1.4585 L23: 2.3226 REMARK 3 S TENSOR REMARK 3 S11: -0.1310 S12: -0.0463 S13: -0.1085 REMARK 3 S21: 0.0157 S22: 0.2328 S23: -0.7259 REMARK 3 S31: -0.2256 S32: 0.6884 S33: -0.0902 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 46 THROUGH 86 ) REMARK 3 ORIGIN FOR THE GROUP (A): -31.8582 -23.2877 -10.8971 REMARK 3 T TENSOR REMARK 3 T11: 0.3401 T22: 0.3745 REMARK 3 T33: 0.3963 T12: 0.0534 REMARK 3 T13: 0.0605 T23: -0.0591 REMARK 3 L TENSOR REMARK 3 L11: 9.1033 L22: 6.8370 REMARK 3 L33: 3.3897 L12: 5.9676 REMARK 3 L13: 1.3802 L23: -0.9654 REMARK 3 S TENSOR REMARK 3 S11: 0.0622 S12: -0.3087 S13: -0.0356 REMARK 3 S21: -0.3469 S22: -0.2620 S23: -0.6223 REMARK 3 S31: -0.1960 S32: 0.3059 S33: 0.1600 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 87 THROUGH 120 ) REMARK 3 ORIGIN FOR THE GROUP (A): -38.4787 -14.0810 -11.1636 REMARK 3 T TENSOR REMARK 3 T11: 0.3185 T22: 0.3325 REMARK 3 T33: 0.3296 T12: -0.0795 REMARK 3 T13: -0.0448 T23: 0.0148 REMARK 3 L TENSOR REMARK 3 L11: 2.9902 L22: 7.1372 REMARK 3 L33: 4.5426 L12: -2.6614 REMARK 3 L13: -1.1374 L23: 2.2649 REMARK 3 S TENSOR REMARK 3 S11: -0.1454 S12: 0.0361 S13: 0.1581 REMARK 3 S21: -0.4272 S22: 0.3546 S23: -0.4266 REMARK 3 S31: -0.1399 S32: 0.3757 S33: -0.2064 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 121 THROUGH 157 ) REMARK 3 ORIGIN FOR THE GROUP (A): -45.3168 1.5054 12.3140 REMARK 3 T TENSOR REMARK 3 T11: 0.7655 T22: 0.3367 REMARK 3 T33: 0.3987 T12: 0.0202 REMARK 3 T13: 0.0046 T23: -0.0377 REMARK 3 L TENSOR REMARK 3 L11: 5.7713 L22: 4.1830 REMARK 3 L33: 7.6964 L12: 1.2510 REMARK 3 L13: -0.5476 L23: 0.2920 REMARK 3 S TENSOR REMARK 3 S11: -0.1830 S12: -0.5151 S13: 0.4377 REMARK 3 S21: 1.2098 S22: -0.0542 S23: 0.4511 REMARK 3 S31: -0.2886 S32: 0.2632 S33: 0.2277 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 158 THROUGH 184 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.8609 -2.0432 14.2295 REMARK 3 T TENSOR REMARK 3 T11: 0.7054 T22: 0.5323 REMARK 3 T33: 0.5377 T12: 0.0377 REMARK 3 T13: -0.1684 T23: -0.1355 REMARK 3 L TENSOR REMARK 3 L11: 7.4926 L22: 9.0162 REMARK 3 L33: 5.5734 L12: -2.4702 REMARK 3 L13: -0.9025 L23: 2.2310 REMARK 3 S TENSOR REMARK 3 S11: -0.0745 S12: -0.7826 S13: 0.3091 REMARK 3 S21: 1.1364 S22: 0.6524 S23: -1.2363 REMARK 3 S31: -0.1935 S32: 0.5462 S33: -0.5422 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 185 THROUGH 206 ) REMARK 3 ORIGIN FOR THE GROUP (A): -46.2753 -10.9470 8.6667 REMARK 3 T TENSOR REMARK 3 T11: 0.4338 T22: 0.3121 REMARK 3 T33: 0.3458 T12: -0.0406 REMARK 3 T13: 0.0087 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 4.5231 L22: 2.3039 REMARK 3 L33: 5.9181 L12: -2.8017 REMARK 3 L13: -0.5626 L23: 2.1282 REMARK 3 S TENSOR REMARK 3 S11: -0.2164 S12: -0.2718 S13: 0.0121 REMARK 3 S21: 0.6667 S22: -0.0708 S23: 0.6902 REMARK 3 S31: 0.0450 S32: -0.1852 S33: 0.2489 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 207 THROUGH 256 ) REMARK 3 ORIGIN FOR THE GROUP (A): -45.3002 -10.5925 -12.1819 REMARK 3 T TENSOR REMARK 3 T11: 0.3090 T22: 0.3088 REMARK 3 T33: 0.2984 T12: -0.0465 REMARK 3 T13: -0.0874 T23: 0.0484 REMARK 3 L TENSOR REMARK 3 L11: 1.6626 L22: 7.2333 REMARK 3 L33: 1.3060 L12: -1.4625 REMARK 3 L13: 0.2377 L23: 1.5209 REMARK 3 S TENSOR REMARK 3 S11: -0.1299 S12: 0.1256 S13: 0.0268 REMARK 3 S21: -0.4015 S22: 0.0316 S23: 0.2961 REMARK 3 S31: -0.2532 S32: 0.0381 S33: 0.1156 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 257 THROUGH 298 ) REMARK 3 ORIGIN FOR THE GROUP (A): -49.5921 3.8068 -7.8958 REMARK 3 T TENSOR REMARK 3 T11: 0.4275 T22: 0.2873 REMARK 3 T33: 0.3580 T12: 0.0220 REMARK 3 T13: -0.0514 T23: 0.0582 REMARK 3 L TENSOR REMARK 3 L11: 6.1107 L22: 6.6423 REMARK 3 L33: 5.7689 L12: 1.8040 REMARK 3 L13: 2.9930 L23: 1.6104 REMARK 3 S TENSOR REMARK 3 S11: -0.1577 S12: 0.1236 S13: 0.3522 REMARK 3 S21: -0.2961 S22: -0.0831 S23: 0.5102 REMARK 3 S31: -0.5401 S32: -0.1232 S33: 0.2726 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 299 THROUGH 357 ) REMARK 3 ORIGIN FOR THE GROUP (A): -45.4550 0.5214 -16.8692 REMARK 3 T TENSOR REMARK 3 T11: 0.4907 T22: 0.3755 REMARK 3 T33: 0.4018 T12: -0.0346 REMARK 3 T13: -0.1402 T23: 0.1048 REMARK 3 L TENSOR REMARK 3 L11: 1.1233 L22: 5.9914 REMARK 3 L33: 4.1091 L12: 0.7999 REMARK 3 L13: 0.2289 L23: 3.3207 REMARK 3 S TENSOR REMARK 3 S11: -0.0782 S12: -0.0030 S13: 0.2066 REMARK 3 S21: -0.6410 S22: -0.0883 S23: 0.0205 REMARK 3 S31: -0.4857 S32: 0.1499 S33: 0.1446 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 7CCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1300017398. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.3 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 : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53490 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 43.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 10.7300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45200 REMARK 200 FOR SHELL : 2.310 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: 3ECR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, DIAMMONIUM HYDROGEN CITRATE, REMARK 280 DITHIOTHREITOL, PH 8.3, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 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 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 35.20550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.59700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.40750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.59700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.20550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.40750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 1 REMARK 465 SER A 2 REMARK 465 GLY A 3 REMARK 465 ASN A 4 REMARK 465 GLY A 5 REMARK 465 ASN A 6 REMARK 465 ALA A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 THR A 10 REMARK 465 ALA A 11 REMARK 465 GLU A 12 REMARK 465 GLU A 13 REMARK 465 ASN A 14 REMARK 465 SER A 15 REMARK 465 PRO A 16 REMARK 465 LYS A 17 REMARK 465 THR A 58 REMARK 465 THR A 59 REMARK 465 GLY A 60 REMARK 465 ASP A 61 REMARK 465 LYS A 62 REMARK 465 ILE A 63 REMARK 465 LEU A 64 REMARK 465 ASP A 65 REMARK 465 THR A 66 REMARK 465 ALA A 67 REMARK 465 LEU A 68 REMARK 465 SER A 69 REMARK 465 LYS A 70 REMARK 465 ILE A 71 REMARK 465 GLY A 72 REMARK 465 GLU A 73 REMARK 465 LYS A 74 REMARK 465 SER A 75 REMARK 465 LEU A 76 REMARK 465 ARG A 355 REMARK 465 GLN A 356 REMARK 465 LEU A 357 REMARK 465 ASN A 358 REMARK 465 ASP A 359 REMARK 465 ALA A 360 REMARK 465 HIS A 361 REMARK 465 MET C 1 REMARK 465 SER C 2 REMARK 465 GLY C 3 REMARK 465 ASN C 4 REMARK 465 GLY C 5 REMARK 465 ASN C 6 REMARK 465 ALA C 7 REMARK 465 ALA C 8 REMARK 465 ALA C 9 REMARK 465 THR C 10 REMARK 465 ALA C 11 REMARK 465 GLU C 12 REMARK 465 GLU C 13 REMARK 465 ASN C 14 REMARK 465 SER C 15 REMARK 465 PRO C 16 REMARK 465 LYS C 17 REMARK 465 SER C 57 REMARK 465 THR C 58 REMARK 465 THR C 59 REMARK 465 GLY C 60 REMARK 465 ASP C 61 REMARK 465 LYS C 62 REMARK 465 ILE C 63 REMARK 465 LEU C 64 REMARK 465 ASP C 65 REMARK 465 THR C 66 REMARK 465 ALA C 67 REMARK 465 LEU C 68 REMARK 465 SER C 69 REMARK 465 LYS C 70 REMARK 465 ILE C 71 REMARK 465 GLY C 72 REMARK 465 GLU C 73 REMARK 465 LYS C 74 REMARK 465 GLN C 181 REMARK 465 VAL C 301 REMARK 465 PRO C 302 REMARK 465 ALA C 303 REMARK 465 GLN C 304 REMARK 465 HIS C 305 REMARK 465 GLU C 306 REMARK 465 ASP C 307 REMARK 465 GLY C 308 REMARK 465 PRO C 309 REMARK 465 GLU C 310 REMARK 465 ASP C 311 REMARK 465 ASP C 312 REMARK 465 ASN C 358 REMARK 465 ASP C 359 REMARK 465 ALA C 360 REMARK 465 HIS C 361 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 ARG A 19 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 GLN A 50 CG CD OE1 NE2 REMARK 470 PHE A 77 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 79 CG CD CE NZ REMARK 470 GLU A 80 CG CD OE1 OE2 REMARK 470 LYS A 227 CG CD CE NZ REMARK 470 GLN A 229 CG CD OE1 NE2 REMARK 470 GLU A 258 CG CD OE1 OE2 REMARK 470 GLN A 304 CG CD OE1 NE2 REMARK 470 GLU A 310 CG CD OE1 OE2 REMARK 470 ASP A 311 CG OD1 OD2 REMARK 470 ARG C 19 CG CD NE CZ NH1 NH2 REMARK 470 PHE C 77 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU C 80 CG CD OE1 OE2 REMARK 470 GLU C 86 CG CD OE1 OE2 REMARK 470 VAL C 130 CG1 CG2 REMARK 470 LYS C 132 CG CD CE NZ REMARK 470 GLU C 139 CG CD OE1 OE2 REMARK 470 LYS C 140 CG CD CE NZ REMARK 470 ARG C 167 CG CD NE CZ NH1 NH2 REMARK 470 ASN C 169 CG OD1 ND2 REMARK 470 GLU C 179 CG CD OE1 OE2 REMARK 470 GLN C 180 CG CD OE1 NE2 REMARK 470 ARG C 201 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 229 CG CD OE1 NE2 REMARK 470 LYS C 272 CG CD CE NZ REMARK 470 GLN C 356 CG CD OE1 NE2 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 ARG A 19 -69.43 -125.68 REMARK 500 CYS A 211 104.12 -162.47 REMARK 500 VAL A 316 48.11 34.01 REMARK 500 CYS C 211 113.27 -160.20 REMARK 500 SER C 262 32.71 -96.17 REMARK 500 ILE C 299 69.98 -113.77 REMARK 500 VAL C 316 45.83 33.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DPM A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide DPM C 401 and CYS C REMARK 800 261 DBREF 7CCX A 1 361 UNP P08397 HEM3_HUMAN 1 361 DBREF 7CCX C 1 361 UNP P08397 HEM3_HUMAN 1 361 SEQRES 1 A 361 MET SER GLY ASN GLY ASN ALA ALA ALA THR ALA GLU GLU SEQRES 2 A 361 ASN SER PRO LYS MET ARG VAL ILE ARG VAL GLY THR ARG SEQRES 3 A 361 LYS SER GLN LEU ALA ARG ILE GLN THR ASP SER VAL VAL SEQRES 4 A 361 ALA THR LEU LYS ALA SER TYR PRO GLY LEU GLN PHE GLU SEQRES 5 A 361 ILE ILE ALA MET SER THR THR GLY ASP LYS ILE LEU ASP SEQRES 6 A 361 THR ALA LEU SER LYS ILE GLY GLU LYS SER LEU PHE THR SEQRES 7 A 361 LYS GLU LEU GLU HIS ALA LEU GLU LYS ASN GLU VAL ASP SEQRES 8 A 361 LEU VAL VAL HIS SER LEU LYS ASP LEU PRO THR VAL LEU SEQRES 9 A 361 PRO PRO GLY PHE THR ILE GLY ALA ILE CYS LYS ARG GLU SEQRES 10 A 361 ASN PRO HIS ASP ALA VAL VAL PHE HIS PRO LYS PHE VAL SEQRES 11 A 361 GLY LYS THR LEU GLU THR LEU PRO GLU LYS SER VAL VAL SEQRES 12 A 361 GLY THR SER SER LEU ARG ARG ALA ALA GLN LEU GLN ARG SEQRES 13 A 361 LYS PHE PRO HIS LEU GLU PHE ARG SER ILE ARG GLY ASN SEQRES 14 A 361 LEU ASN THR ARG LEU ARG LYS LEU ASP GLU GLN GLN GLU SEQRES 15 A 361 PHE SER ALA ILE ILE LEU ALA THR ALA GLY LEU GLN ARG SEQRES 16 A 361 MET GLY TRP HIS ASN ARG VAL GLY GLN ILE LEU HIS PRO SEQRES 17 A 361 GLU GLU CYS MET TYR ALA VAL GLY GLN GLY ALA LEU GLY SEQRES 18 A 361 VAL GLU VAL ARG ALA LYS ASP GLN ASP ILE LEU ASP LEU SEQRES 19 A 361 VAL GLY VAL LEU HIS ASP PRO GLU THR LEU LEU ARG CYS SEQRES 20 A 361 ILE ALA GLU ARG ALA PHE LEU ARG HIS LEU GLU GLY GLY SEQRES 21 A 361 CYS SER VAL PRO VAL ALA VAL HIS THR ALA MET LYS ASP SEQRES 22 A 361 GLY GLN LEU TYR LEU THR GLY GLY VAL TRP SER LEU ASP SEQRES 23 A 361 GLY SER ASP SER ILE GLN GLU THR MET GLN ALA THR ILE SEQRES 24 A 361 HIS VAL PRO ALA GLN HIS GLU ASP GLY PRO GLU ASP ASP SEQRES 25 A 361 PRO GLN LEU VAL GLY ILE THR ALA ARG ASN ILE PRO ARG SEQRES 26 A 361 GLY PRO GLN LEU ALA ALA GLN ASN LEU GLY ILE SER LEU SEQRES 27 A 361 ALA ASN LEU LEU LEU SER LYS GLY ALA LYS ASN ILE LEU SEQRES 28 A 361 ASP VAL ALA ARG GLN LEU ASN ASP ALA HIS SEQRES 1 C 361 MET SER GLY ASN GLY ASN ALA ALA ALA THR ALA GLU GLU SEQRES 2 C 361 ASN SER PRO LYS MET ARG VAL ILE ARG VAL GLY THR ARG SEQRES 3 C 361 LYS SER GLN LEU ALA ARG ILE GLN THR ASP SER VAL VAL SEQRES 4 C 361 ALA THR LEU LYS ALA SER TYR PRO GLY LEU GLN PHE GLU SEQRES 5 C 361 ILE ILE ALA MET SER THR THR GLY ASP LYS ILE LEU ASP SEQRES 6 C 361 THR ALA LEU SER LYS ILE GLY GLU LYS SER LEU PHE THR SEQRES 7 C 361 LYS GLU LEU GLU HIS ALA LEU GLU LYS ASN GLU VAL ASP SEQRES 8 C 361 LEU VAL VAL HIS SER LEU LYS ASP LEU PRO THR VAL LEU SEQRES 9 C 361 PRO PRO GLY PHE THR ILE GLY ALA ILE CYS LYS ARG GLU SEQRES 10 C 361 ASN PRO HIS ASP ALA VAL VAL PHE HIS PRO LYS PHE VAL SEQRES 11 C 361 GLY LYS THR LEU GLU THR LEU PRO GLU LYS SER VAL VAL SEQRES 12 C 361 GLY THR SER SER LEU ARG ARG ALA ALA GLN LEU GLN ARG SEQRES 13 C 361 LYS PHE PRO HIS LEU GLU PHE ARG SER ILE ARG GLY ASN SEQRES 14 C 361 LEU ASN THR ARG LEU ARG LYS LEU ASP GLU GLN GLN GLU SEQRES 15 C 361 PHE SER ALA ILE ILE LEU ALA THR ALA GLY LEU GLN ARG SEQRES 16 C 361 MET GLY TRP HIS ASN ARG VAL GLY GLN ILE LEU HIS PRO SEQRES 17 C 361 GLU GLU CYS MET TYR ALA VAL GLY GLN GLY ALA LEU GLY SEQRES 18 C 361 VAL GLU VAL ARG ALA LYS ASP GLN ASP ILE LEU ASP LEU SEQRES 19 C 361 VAL GLY VAL LEU HIS ASP PRO GLU THR LEU LEU ARG CYS SEQRES 20 C 361 ILE ALA GLU ARG ALA PHE LEU ARG HIS LEU GLU GLY GLY SEQRES 21 C 361 CYS SER VAL PRO VAL ALA VAL HIS THR ALA MET LYS ASP SEQRES 22 C 361 GLY GLN LEU TYR LEU THR GLY GLY VAL TRP SER LEU ASP SEQRES 23 C 361 GLY SER ASP SER ILE GLN GLU THR MET GLN ALA THR ILE SEQRES 24 C 361 HIS VAL PRO ALA GLN HIS GLU ASP GLY PRO GLU ASP ASP SEQRES 25 C 361 PRO GLN LEU VAL GLY ILE THR ALA ARG ASN ILE PRO ARG SEQRES 26 C 361 GLY PRO GLN LEU ALA ALA GLN ASN LEU GLY ILE SER LEU SEQRES 27 C 361 ALA ASN LEU LEU LEU SER LYS GLY ALA LYS ASN ILE LEU SEQRES 28 C 361 ASP VAL ALA ARG GLN LEU ASN ASP ALA HIS HET DPM A 401 30 HET DPM C 401 30 HETNAM DPM 3-[5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5-METHYL- HETNAM 2 DPM 1H-PYRROL-2-YL]METHYL}-4-(CARBOXYMETHYL)-1H-PYRROL-3- HETNAM 3 DPM YL]PROPANOIC ACID HETSYN DPM DIPYRROMETHANE COFACTOR FORMUL 3 DPM 2(C20 H24 N2 O8) FORMUL 5 HOH *159(H2 O) HELIX 1 AA1 SER A 28 TYR A 46 1 19 HELIX 2 AA2 THR A 78 LYS A 87 1 10 HELIX 3 AA3 LYS A 98 LEU A 100 5 3 HELIX 4 AA4 PRO A 127 VAL A 130 5 4 HELIX 5 AA5 THR A 133 LEU A 137 5 5 HELIX 6 AA6 SER A 147 PHE A 158 1 12 HELIX 7 AA7 ASN A 169 GLN A 180 1 12 HELIX 8 AA8 THR A 190 MET A 196 1 7 HELIX 9 AA9 TRP A 198 VAL A 202 5 5 HELIX 10 AB1 ASP A 228 GLY A 236 1 9 HELIX 11 AB2 VAL A 237 HIS A 239 5 3 HELIX 12 AB3 ASP A 240 LEU A 257 1 18 HELIX 13 AB4 PRO A 324 LYS A 345 1 22 HELIX 14 AB5 GLY A 346 ALA A 354 1 9 HELIX 15 AB6 SER C 28 TYR C 46 1 19 HELIX 16 AB7 LEU C 76 LYS C 87 1 12 HELIX 17 AB8 LYS C 98 LEU C 100 5 3 HELIX 18 AB9 PRO C 127 VAL C 130 5 4 HELIX 19 AC1 SER C 147 PHE C 158 1 12 HELIX 20 AC2 ASN C 169 GLN C 180 1 12 HELIX 21 AC3 THR C 190 GLY C 197 1 8 HELIX 22 AC4 TRP C 198 VAL C 202 5 5 HELIX 23 AC5 ASP C 228 GLY C 236 1 9 HELIX 24 AC6 VAL C 237 HIS C 239 5 3 HELIX 25 AC7 ASP C 240 LEU C 257 1 18 HELIX 26 AC8 PRO C 324 LYS C 345 1 22 HELIX 27 AC9 GLY C 346 LEU C 357 1 12 SHEET 1 AA1 5 GLN A 50 MET A 56 0 SHEET 2 AA1 5 VAL A 20 ARG A 26 1 N VAL A 23 O GLU A 52 SHEET 3 AA1 5 LEU A 92 SER A 96 1 O LEU A 92 N GLY A 24 SHEET 4 AA1 5 LEU A 220 ARG A 225 -1 O GLY A 221 N HIS A 95 SHEET 5 AA1 5 PHE A 108 ILE A 113 -1 N THR A 109 O VAL A 224 SHEET 1 AA2 5 GLU A 162 ARG A 164 0 SHEET 2 AA2 5 VAL A 142 GLY A 144 1 N VAL A 143 O GLU A 162 SHEET 3 AA2 5 ALA A 185 ALA A 189 1 O ALA A 185 N GLY A 144 SHEET 4 AA2 5 ASP A 121 PHE A 125 -1 N ALA A 122 O LEU A 188 SHEET 5 AA2 5 GLN A 204 ILE A 205 -1 O GLN A 204 N VAL A 123 SHEET 1 AA3 3 VAL A 265 LYS A 272 0 SHEET 2 AA3 3 GLN A 275 TRP A 283 -1 O THR A 279 N HIS A 268 SHEET 3 AA3 3 SER A 290 THR A 298 -1 O MET A 295 N LEU A 278 SHEET 1 AA4 5 GLN C 50 ALA C 55 0 SHEET 2 AA4 5 VAL C 20 THR C 25 1 N VAL C 23 O ILE C 54 SHEET 3 AA4 5 LEU C 92 SER C 96 1 O LEU C 92 N GLY C 24 SHEET 4 AA4 5 LEU C 220 ARG C 225 -1 O GLY C 221 N HIS C 95 SHEET 5 AA4 5 PHE C 108 ILE C 113 -1 N THR C 109 O VAL C 224 SHEET 1 AA5 5 GLU C 162 ARG C 164 0 SHEET 2 AA5 5 VAL C 142 GLY C 144 1 N VAL C 143 O GLU C 162 SHEET 3 AA5 5 ALA C 185 ALA C 189 1 O ALA C 185 N GLY C 144 SHEET 4 AA5 5 ASP C 121 PHE C 125 -1 N ALA C 122 O LEU C 188 SHEET 5 AA5 5 GLN C 204 ILE C 205 -1 O GLN C 204 N VAL C 123 SHEET 1 AA6 3 VAL C 265 LYS C 272 0 SHEET 2 AA6 3 GLN C 275 TRP C 283 -1 O TYR C 277 N ALA C 270 SHEET 3 AA6 3 SER C 290 THR C 298 -1 O MET C 295 N LEU C 278 LINK SG CYS A 261 CHA DPM A 401 1555 1555 1.62 LINK SG CYS C 261 CHA DPM C 401 1555 1555 1.61 SITE 1 AC1 19 SER A 96 LYS A 98 ASP A 99 SER A 146 SITE 2 AC1 19 SER A 147 ARG A 149 ARG A 150 ARG A 173 SITE 3 AC1 19 LEU A 188 ALA A 189 ARG A 195 GLN A 217 SITE 4 AC1 19 GLY A 218 CYS A 261 HOH A 511 HOH A 525 SITE 5 AC1 19 HOH A 534 HOH A 561 HOH A 575 SITE 1 AC2 20 SER C 96 LYS C 98 ASP C 99 SER C 146 SITE 2 AC2 20 SER C 147 ARG C 149 ARG C 150 ARG C 173 SITE 3 AC2 20 LEU C 188 ALA C 189 ALA C 214 GLN C 217 SITE 4 AC2 20 GLY C 218 GLY C 260 SER C 262 VAL C 263 SITE 5 AC2 20 HOH C 501 HOH C 507 HOH C 517 HOH C 534 CRYST1 70.411 80.815 109.194 90.00 90.00 90.00 P 21 21 21 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 0.014202 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012374 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009158 0.00000