HEADER TRANSFERASE 18-JUN-20 7CD0 TITLE CRYSTAL STRUCTURE OF THE 2-IODOPORPHOBILINOGEN-BOUND ES2 INTERMEDIATE TITLE 2 FORM OF HUMAN HYDROXYMETHYLBILANE SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PORPHOBILINOGEN DEAMINASE; COMPND 3 CHAIN: A, B; 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 3 23-OCT-24 7CD0 1 REMARK REVDAT 2 29-NOV-23 7CD0 1 REMARK REVDAT 1 17-MAR-21 7CD0 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. 2.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 32256 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1612 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 45.2500 - 5.2900 1.00 2732 144 0.1923 0.2102 REMARK 3 2 5.2800 - 4.1900 1.00 2628 138 0.1710 0.2102 REMARK 3 3 4.1900 - 3.6700 1.00 2571 135 0.1937 0.2490 REMARK 3 4 3.6600 - 3.3300 1.00 2563 135 0.2161 0.3065 REMARK 3 5 3.3300 - 3.0900 1.00 2549 135 0.2447 0.3037 REMARK 3 6 3.0900 - 2.9100 1.00 2554 134 0.2522 0.2653 REMARK 3 7 2.9100 - 2.7600 1.00 2550 134 0.2769 0.3199 REMARK 3 8 2.7600 - 2.6400 1.00 2527 133 0.2923 0.3778 REMARK 3 9 2.6400 - 2.5400 1.00 2542 134 0.3201 0.3446 REMARK 3 10 2.5400 - 2.4500 1.00 2517 132 0.3436 0.4345 REMARK 3 11 2.4500 - 2.3800 1.00 2544 134 0.3456 0.4590 REMARK 3 12 2.3800 - 2.3100 0.95 2367 124 0.3702 0.4481 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) : 0.317 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.402 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.52 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 5121 REMARK 3 ANGLE : 1.011 6955 REMARK 3 CHIRALITY : 0.059 796 REMARK 3 PLANARITY : 0.009 909 REMARK 3 DIHEDRAL : 21.957 1900 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 19 THROUGH 86 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.5079 28.5323 1.3063 REMARK 3 T TENSOR REMARK 3 T11: 0.3144 T22: 0.3659 REMARK 3 T33: 0.3422 T12: 0.0437 REMARK 3 T13: 0.0112 T23: 0.0431 REMARK 3 L TENSOR REMARK 3 L11: 1.5026 L22: 4.5630 REMARK 3 L33: 6.5456 L12: 0.1325 REMARK 3 L13: -2.4357 L23: -1.5467 REMARK 3 S TENSOR REMARK 3 S11: -0.1592 S12: -0.2506 S13: -0.3523 REMARK 3 S21: 0.1145 S22: 0.0428 S23: 0.1067 REMARK 3 S31: 0.8137 S32: -0.1772 S33: 0.0959 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 87 THROUGH 206 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.4449 33.3460 -13.6874 REMARK 3 T TENSOR REMARK 3 T11: 0.2660 T22: 0.2367 REMARK 3 T33: 0.2919 T12: -0.0048 REMARK 3 T13: 0.0534 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 5.0460 L22: 0.4362 REMARK 3 L33: 6.1426 L12: 0.1594 REMARK 3 L13: 1.7724 L23: 0.7287 REMARK 3 S TENSOR REMARK 3 S11: 0.0109 S12: 0.4831 S13: -0.1270 REMARK 3 S21: -0.0644 S22: -0.0328 S23: 0.0499 REMARK 3 S31: 0.0299 S32: -0.2152 S33: 0.0025 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 207 THROUGH 257 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.6278 39.5959 4.2618 REMARK 3 T TENSOR REMARK 3 T11: 0.2549 T22: 0.2385 REMARK 3 T33: 0.2481 T12: -0.0607 REMARK 3 T13: 0.0104 T23: -0.0684 REMARK 3 L TENSOR REMARK 3 L11: 6.4950 L22: 1.6871 REMARK 3 L33: 2.9071 L12: -0.7629 REMARK 3 L13: 0.8978 L23: 0.5721 REMARK 3 S TENSOR REMARK 3 S11: 0.0402 S12: -0.1769 S13: 0.6736 REMARK 3 S21: 0.0990 S22: -0.0608 S23: -0.0411 REMARK 3 S31: -0.1410 S32: 0.1156 S33: 0.0595 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 258 THROUGH 298 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.8973 43.3866 -0.8583 REMARK 3 T TENSOR REMARK 3 T11: 0.2113 T22: 0.4018 REMARK 3 T33: 0.2401 T12: 0.0317 REMARK 3 T13: 0.0445 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 6.4239 L22: 8.0038 REMARK 3 L33: 6.6331 L12: 2.0800 REMARK 3 L13: 1.7533 L23: 3.8021 REMARK 3 S TENSOR REMARK 3 S11: -0.2944 S12: 0.1949 S13: 0.3400 REMARK 3 S21: 0.0113 S22: 0.0466 S23: 0.3067 REMARK 3 S31: -0.2372 S32: -0.3183 S33: 0.1835 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 299 THROUGH 358 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.4490 41.2042 9.9359 REMARK 3 T TENSOR REMARK 3 T11: 0.2900 T22: 0.3684 REMARK 3 T33: 0.1734 T12: 0.0790 REMARK 3 T13: 0.0748 T23: 0.0130 REMARK 3 L TENSOR REMARK 3 L11: 9.5571 L22: 3.7441 REMARK 3 L33: 5.4717 L12: 1.9768 REMARK 3 L13: 1.9439 L23: 1.0874 REMARK 3 S TENSOR REMARK 3 S11: -0.1316 S12: -0.7310 S13: 0.1816 REMARK 3 S21: 0.0477 S22: 0.0660 S23: -0.2388 REMARK 3 S31: 0.1360 S32: 0.0444 S33: 0.0177 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 19 THROUGH 99 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.0880 22.3325 -35.9860 REMARK 3 T TENSOR REMARK 3 T11: 0.3700 T22: 0.4150 REMARK 3 T33: 0.4225 T12: -0.0808 REMARK 3 T13: 0.0814 T23: 0.0245 REMARK 3 L TENSOR REMARK 3 L11: 4.7081 L22: 4.1861 REMARK 3 L33: 3.0367 L12: 0.7144 REMARK 3 L13: -1.0099 L23: 1.8795 REMARK 3 S TENSOR REMARK 3 S11: -0.2569 S12: 0.2386 S13: -0.8429 REMARK 3 S21: -0.0051 S22: -0.1154 S23: 0.0637 REMARK 3 S31: 0.4917 S32: -0.1399 S33: 0.3004 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 100 THROUGH 228 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.3519 29.1862 -21.1938 REMARK 3 T TENSOR REMARK 3 T11: 0.2798 T22: 0.4536 REMARK 3 T33: 0.3751 T12: 0.0586 REMARK 3 T13: 0.0288 T23: 0.0930 REMARK 3 L TENSOR REMARK 3 L11: 3.2485 L22: 1.2923 REMARK 3 L33: 5.9832 L12: 0.1166 REMARK 3 L13: 0.8253 L23: -0.0930 REMARK 3 S TENSOR REMARK 3 S11: -0.0996 S12: -0.4122 S13: -0.1939 REMARK 3 S21: 0.2391 S22: 0.0058 S23: -0.2308 REMARK 3 S31: 0.1683 S32: 0.4321 S33: 0.0871 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 229 THROUGH 283 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.9549 35.2986 -39.1383 REMARK 3 T TENSOR REMARK 3 T11: 0.2692 T22: 0.4306 REMARK 3 T33: 0.2712 T12: 0.0386 REMARK 3 T13: 0.0339 T23: 0.1496 REMARK 3 L TENSOR REMARK 3 L11: 7.0790 L22: 1.9920 REMARK 3 L33: 4.1565 L12: 2.6722 REMARK 3 L13: 1.0137 L23: 0.1830 REMARK 3 S TENSOR REMARK 3 S11: -0.0294 S12: 0.1260 S13: 0.2107 REMARK 3 S21: -0.0374 S22: -0.0328 S23: 0.0474 REMARK 3 S31: -0.2303 S32: 0.2279 S33: 0.0664 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 284 THROUGH 357 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.5066 35.2175 -42.4922 REMARK 3 T TENSOR REMARK 3 T11: 0.2427 T22: 0.4331 REMARK 3 T33: 0.2833 T12: 0.0011 REMARK 3 T13: 0.0998 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 5.3766 L22: 3.8979 REMARK 3 L33: 4.5108 L12: 0.3670 REMARK 3 L13: 0.2589 L23: -1.1914 REMARK 3 S TENSOR REMARK 3 S11: -0.1864 S12: 0.3491 S13: 0.0351 REMARK 3 S21: -0.0770 S22: 0.0947 S23: 0.0432 REMARK 3 S31: -0.1191 S32: 0.1659 S33: 0.0664 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (chain "A" and (resid 19 through 57 or REMARK 3 resid 77 through 78 or (resid 79 through REMARK 3 80 and (name N or name CA or name C or REMARK 3 name O or name CB )) or resid 81 through REMARK 3 88 or (resid 89 and (name N or name CA or REMARK 3 name C or name O or name CB )) or resid REMARK 3 90 through 134 or (resid 135 and (name N REMARK 3 or name CA or name C or name O or name CB REMARK 3 )) or resid 136 through 166 or (resid 167 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB )) or resid 168 through 208 REMARK 3 or (resid 209 and (name N or name CA or REMARK 3 name C or name O or name CB )) or resid REMARK 3 210 through 357)) REMARK 3 SELECTION : (chain "B" and ((resid 19 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 20 through 49 or (resid 50 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 51 through 81 or REMARK 3 (resid 82 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 83 REMARK 3 through 303 or (resid 304 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 305 through 357)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : 0.958918539558 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7CD0 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_1300017405. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-18 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) : 1.5 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32296 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.310 REMARK 200 RESOLUTION RANGE LOW (A) : 45.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08400 REMARK 200 FOR THE DATA SET : 5.4800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38800 REMARK 200 FOR SHELL : 1.460 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 (%): 46.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 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 40.70800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.42500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.68300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.42500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.70800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.68300 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: B 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 MET A 18 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 ASP A 359 REMARK 465 ALA A 360 REMARK 465 HIS A 361 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 GLY B 3 REMARK 465 ASN B 4 REMARK 465 GLY B 5 REMARK 465 ASN B 6 REMARK 465 ALA B 7 REMARK 465 ALA B 8 REMARK 465 ALA B 9 REMARK 465 THR B 10 REMARK 465 ALA B 11 REMARK 465 GLU B 12 REMARK 465 GLU B 13 REMARK 465 ASN B 14 REMARK 465 SER B 15 REMARK 465 PRO B 16 REMARK 465 LYS B 17 REMARK 465 MET B 18 REMARK 465 THR B 58 REMARK 465 THR B 59 REMARK 465 GLY B 60 REMARK 465 ASP B 61 REMARK 465 LYS B 62 REMARK 465 ILE B 63 REMARK 465 LEU B 64 REMARK 465 ASP B 65 REMARK 465 THR B 66 REMARK 465 ALA B 67 REMARK 465 LEU B 68 REMARK 465 SER B 69 REMARK 465 LYS B 70 REMARK 465 ILE B 71 REMARK 465 GLY B 72 REMARK 465 GLU B 73 REMARK 465 LYS B 74 REMARK 465 SER B 75 REMARK 465 LEU B 76 REMARK 465 ASN B 358 REMARK 465 ASP B 359 REMARK 465 ALA B 360 REMARK 465 HIS B 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 GLN A 50 CG CD OE1 NE2 REMARK 470 GLU A 80 CG CD OE1 OE2 REMARK 470 GLU A 82 CG CD OE1 OE2 REMARK 470 LYS A 227 CG CD CE NZ REMARK 470 LYS A 272 CG CD CE NZ REMARK 470 GLN A 304 CG CD OE1 NE2 REMARK 470 GLU A 310 CG CD OE1 OE2 REMARK 470 LYS B 79 CG CD CE NZ REMARK 470 GLU B 80 CG CD OE1 OE2 REMARK 470 GLU B 89 CG CD OE1 OE2 REMARK 470 GLU B 135 CG CD OE1 OE2 REMARK 470 ARG B 167 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 209 CG CD OE1 OE2 REMARK 470 LYS B 227 CG CD CE NZ REMARK 470 LYS B 272 CG CD CE NZ REMARK 470 GLU B 310 CG CD OE1 OE2 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 NH1 ARG B 251 O VAL B 316 2.12 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 THR A 145 136.49 -171.07 REMARK 500 SER A 262 72.52 57.89 REMARK 500 VAL A 316 43.93 37.94 REMARK 500 THR B 78 -46.82 -132.78 REMARK 500 THR B 145 139.55 -173.53 REMARK 500 SER B 262 72.47 59.22 REMARK 500 VAL B 316 44.87 38.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 26 0.22 SIDE CHAIN 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 7J8 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FWL B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide 7J8 B 401 and CYS B REMARK 800 261 DBREF 7CD0 A 1 361 UNP P08397 HEM3_HUMAN 1 361 DBREF 7CD0 B 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 B 361 MET SER GLY ASN GLY ASN ALA ALA ALA THR ALA GLU GLU SEQRES 2 B 361 ASN SER PRO LYS MET ARG VAL ILE ARG VAL GLY THR ARG SEQRES 3 B 361 LYS SER GLN LEU ALA ARG ILE GLN THR ASP SER VAL VAL SEQRES 4 B 361 ALA THR LEU LYS ALA SER TYR PRO GLY LEU GLN PHE GLU SEQRES 5 B 361 ILE ILE ALA MET SER THR THR GLY ASP LYS ILE LEU ASP SEQRES 6 B 361 THR ALA LEU SER LYS ILE GLY GLU LYS SER LEU PHE THR SEQRES 7 B 361 LYS GLU LEU GLU HIS ALA LEU GLU LYS ASN GLU VAL ASP SEQRES 8 B 361 LEU VAL VAL HIS SER LEU LYS ASP LEU PRO THR VAL LEU SEQRES 9 B 361 PRO PRO GLY PHE THR ILE GLY ALA ILE CYS LYS ARG GLU SEQRES 10 B 361 ASN PRO HIS ASP ALA VAL VAL PHE HIS PRO LYS PHE VAL SEQRES 11 B 361 GLY LYS THR LEU GLU THR LEU PRO GLU LYS SER VAL VAL SEQRES 12 B 361 GLY THR SER SER LEU ARG ARG ALA ALA GLN LEU GLN ARG SEQRES 13 B 361 LYS PHE PRO HIS LEU GLU PHE ARG SER ILE ARG GLY ASN SEQRES 14 B 361 LEU ASN THR ARG LEU ARG LYS LEU ASP GLU GLN GLN GLU SEQRES 15 B 361 PHE SER ALA ILE ILE LEU ALA THR ALA GLY LEU GLN ARG SEQRES 16 B 361 MET GLY TRP HIS ASN ARG VAL GLY GLN ILE LEU HIS PRO SEQRES 17 B 361 GLU GLU CYS MET TYR ALA VAL GLY GLN GLY ALA LEU GLY SEQRES 18 B 361 VAL GLU VAL ARG ALA LYS ASP GLN ASP ILE LEU ASP LEU SEQRES 19 B 361 VAL GLY VAL LEU HIS ASP PRO GLU THR LEU LEU ARG CYS SEQRES 20 B 361 ILE ALA GLU ARG ALA PHE LEU ARG HIS LEU GLU GLY GLY SEQRES 21 B 361 CYS SER VAL PRO VAL ALA VAL HIS THR ALA MET LYS ASP SEQRES 22 B 361 GLY GLN LEU TYR LEU THR GLY GLY VAL TRP SER LEU ASP SEQRES 23 B 361 GLY SER ASP SER ILE GLN GLU THR MET GLN ALA THR ILE SEQRES 24 B 361 HIS VAL PRO ALA GLN HIS GLU ASP GLY PRO GLU ASP ASP SEQRES 25 B 361 PRO GLN LEU VAL GLY ILE THR ALA ARG ASN ILE PRO ARG SEQRES 26 B 361 GLY PRO GLN LEU ALA ALA GLN ASN LEU GLY ILE SER LEU SEQRES 27 B 361 ALA ASN LEU LEU LEU SER LYS GLY ALA LYS ASN ILE LEU SEQRES 28 B 361 ASP VAL ALA ARG GLN LEU ASN ASP ALA HIS HET 7J8 A 401 60 HET 7J8 B 401 60 HET FWL B 402 17 HETNAM 7J8 3-[4-(2-HYDROXY-2-OXOETHYL)-5-[[4-(2-HYDROXY-2- HETNAM 2 7J8 OXOETHYL)-5-[[4-(2-HYDROXY-2-OXOETHYL)-5-[[4-(2- HETNAM 3 7J8 HYDROXY-2-OXOETHYL)-3-(3-HYDROXY-3-OXOPROPYL)-5- HETNAM 4 7J8 METHYL-1~{H}-PYRROL-2-YL]METHYL]-3-(3-HYDROXY-3- HETNAM 5 7J8 OXOPROPYL)-1~{H}-PYRROL-2-YL]METHYL]-3-(3-HYDROXY-3- HETNAM 6 7J8 OXOPROPYL)-1~{H}-PYRROL-2-YL]METHYL]-1~{H}-PYRROL-3- HETNAM 7 7J8 YL]PROPANOIC ACID HETNAM FWL 3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-2-IODO-1H-PYRROL- HETNAM 2 FWL 3-YL]PROPANOIC ACID HETSYN FWL 2-IODOPORPHOBILINOGEN FORMUL 3 7J8 2(C40 H46 N4 O16) FORMUL 5 FWL C10 H13 I N2 O4 FORMUL 6 HOH *76(H2 O) HELIX 1 AA1 SER A 28 TYR A 46 1 19 HELIX 2 AA2 PHE A 77 LYS A 87 1 11 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 SER A 147 PHE A 158 1 12 HELIX 6 AA6 ASN A 169 GLN A 180 1 12 HELIX 7 AA7 THR A 190 MET A 196 1 7 HELIX 8 AA8 TRP A 198 VAL A 202 5 5 HELIX 9 AA9 ASP A 228 GLY A 236 1 9 HELIX 10 AB1 VAL A 237 HIS A 239 5 3 HELIX 11 AB2 ASP A 240 GLU A 258 1 19 HELIX 12 AB3 PRO A 324 LYS A 345 1 22 HELIX 13 AB4 GLY A 346 LEU A 357 1 12 HELIX 14 AB5 SER B 28 TYR B 46 1 19 HELIX 15 AB6 THR B 78 LYS B 87 1 10 HELIX 16 AB7 LYS B 98 LEU B 100 5 3 HELIX 17 AB8 PRO B 127 VAL B 130 5 4 HELIX 18 AB9 SER B 147 PHE B 158 1 12 HELIX 19 AC1 ASN B 169 GLN B 180 1 12 HELIX 20 AC2 THR B 190 MET B 196 1 7 HELIX 21 AC3 TRP B 198 VAL B 202 5 5 HELIX 22 AC4 ASP B 228 GLY B 236 1 9 HELIX 23 AC5 VAL B 237 HIS B 239 5 3 HELIX 24 AC6 ASP B 240 GLU B 258 1 19 HELIX 25 AC7 PRO B 324 LYS B 345 1 22 HELIX 26 AC8 GLY B 346 GLN B 356 1 11 SHEET 1 AA1 5 PHE A 51 MET A 56 0 SHEET 2 AA1 5 ILE A 21 ARG A 26 1 N VAL A 23 O ILE A 54 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 GLU A 223 N VAL A 93 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 ILE A 187 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 ALA A 297 N LEU A 276 SHEET 1 AA4 5 PHE B 51 MET B 56 0 SHEET 2 AA4 5 ILE B 21 ARG B 26 1 N VAL B 23 O ILE B 54 SHEET 3 AA4 5 LEU B 92 SER B 96 1 O LEU B 92 N GLY B 24 SHEET 4 AA4 5 LEU B 220 ARG B 225 -1 O GLY B 221 N HIS B 95 SHEET 5 AA4 5 PHE B 108 ILE B 113 -1 N THR B 109 O VAL B 224 SHEET 1 AA5 5 GLU B 162 ARG B 164 0 SHEET 2 AA5 5 VAL B 142 GLY B 144 1 N VAL B 143 O ARG B 164 SHEET 3 AA5 5 ALA B 185 ALA B 189 1 O ALA B 185 N GLY B 144 SHEET 4 AA5 5 ASP B 121 PHE B 125 -1 N ALA B 122 O LEU B 188 SHEET 5 AA5 5 GLN B 204 ILE B 205 -1 O GLN B 204 N VAL B 123 SHEET 1 AA6 3 VAL B 265 LYS B 272 0 SHEET 2 AA6 3 GLN B 275 TRP B 283 -1 O THR B 279 N HIS B 268 SHEET 3 AA6 3 SER B 290 THR B 298 -1 O ALA B 297 N LEU B 276 LINK SG CYS A 261 C 7J8 A 401 1555 1555 1.77 LINK SG CYS B 261 C 7J8 B 401 1555 1555 1.77 SITE 1 AC1 25 SER A 96 LYS A 98 ASP A 99 LEU A 100 SITE 2 AC1 25 PRO A 101 THR A 102 SER A 146 SER A 147 SITE 3 AC1 25 ARG A 149 ARG A 150 ARG A 173 LEU A 188 SITE 4 AC1 25 ALA A 189 ARG A 195 VAL A 215 GLY A 218 SITE 5 AC1 25 LEU A 254 GLY A 260 CYS A 261 SER A 262 SITE 6 AC1 25 HOH A 501 HOH A 513 HOH A 529 HOH A 533 SITE 7 AC1 25 HOH A 539 SITE 1 AC2 8 SER B 28 LEU B 30 GLN B 34 ASP B 99 SITE 2 AC2 8 GLY B 168 ASN B 169 LEU B 170 ARG B 173 SITE 1 AC3 23 GLN B 34 SER B 96 LYS B 98 ASP B 99 SITE 2 AC3 23 PRO B 101 THR B 102 THR B 145 SER B 146 SITE 3 AC3 23 SER B 147 ARG B 149 ARG B 150 ARG B 173 SITE 4 AC3 23 LEU B 188 ALA B 189 ARG B 195 VAL B 215 SITE 5 AC3 23 GLY B 218 LEU B 254 GLY B 260 SER B 262 SITE 6 AC3 23 VAL B 263 HOH B 503 HOH B 516 CRYST1 81.416 81.366 108.850 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 0.012283 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012290 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009187 0.00000 MTRIX1 1 -0.999902 0.008060 -0.011435 -0.26390 1 MTRIX2 1 0.008697 0.998343 -0.056875 -6.12386 1 MTRIX3 1 0.010958 -0.056969 -0.998316 -32.30187 1