HEADER TRANSFERASE 18-JUN-20 7CCY TITLE CRYSTAL STRUCTURE OF THE 2-IODOPORPHOBILINOGEN-BOUND HOLO FORM OF TITLE 2 HUMAN HYDROXYMETHYLBILANE 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, INHIBITOR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.SATO,M.SUGISHIMA,K.WADA,K.HIRABAYASHI,M.TSUKAGUCHI REVDAT 2 29-NOV-23 7CCY 1 REMARK REVDAT 1 17-MAR-21 7CCY 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 25874 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1293 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 48.9100 - 4.9900 1.00 2934 155 0.1755 0.2510 REMARK 3 2 4.9900 - 3.9600 1.00 2824 149 0.1460 0.1941 REMARK 3 3 3.9600 - 3.4600 0.99 2756 144 0.1829 0.2329 REMARK 3 4 3.4600 - 3.1500 0.99 2730 143 0.2120 0.3252 REMARK 3 5 3.1500 - 2.9200 0.98 2708 143 0.2305 0.3337 REMARK 3 6 2.9200 - 2.7500 0.98 2673 140 0.2460 0.2906 REMARK 3 7 2.7500 - 2.6100 0.98 2699 142 0.2645 0.3351 REMARK 3 8 2.6100 - 2.5000 0.97 2658 139 0.2779 0.3672 REMARK 3 9 2.5000 - 2.4000 0.95 2599 138 0.2908 0.3788 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.776 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.64 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 : 0.010 5013 REMARK 3 ANGLE : 1.319 6812 REMARK 3 CHIRALITY : 0.067 800 REMARK 3 PLANARITY : 0.008 886 REMARK 3 DIHEDRAL : 20.908 1843 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 : 2 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (chain "A" and (resid 19 through 21 or REMARK 3 (resid 22 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 23 REMARK 3 through 31 or resid 33 through 127 or REMARK 3 (resid 128 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 129 REMARK 3 through 134 or (resid 135 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 136 through 139 or (resid 140 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB )) or resid 141 through 161 REMARK 3 or (resid 162 and (name N or name CA or REMARK 3 name C or name O or name CB )) or resid REMARK 3 163 or (resid 164 and (name N or name CA REMARK 3 or name C or name O or name CB )) or REMARK 3 resid 165 through 228 or (resid 229 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 230 through 254 or REMARK 3 resid 256 through 272 or (resid 273 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 274 through 299 or REMARK 3 resid 313 through 348 or resid 350 REMARK 3 through 354)) REMARK 3 SELECTION : (chain "C" and (resid 19 through 31 or REMARK 3 resid 33 through 61 or (resid 62 and REMARK 3 (name N or name CA or name C or name O or REMARK 3 name CB )) or resid 80 through 86 or REMARK 3 (resid 87 and (name N or name CA or name REMARK 3 C or name O or name CB )) or resid 88 REMARK 3 through 131 or (resid 132 and (name N or REMARK 3 name CA or name C or name O or name CB )) REMARK 3 or resid 133 through 208 or (resid 209 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB )) or resid 210 through 226 REMARK 3 or (resid 227 and (name N or name CA or REMARK 3 name C or name O or name CB )) or resid REMARK 3 228 through 254 or resid 256 through 257 REMARK 3 or (resid 258 and (name N or name CA or REMARK 3 name C or name O or name CB )) or resid REMARK 3 259 through 271 or (resid 272 through 273 REMARK 3 and (name N or name CA or name C or name REMARK 3 O or name CB )) or resid 274 through 299 REMARK 3 or resid 313 through 348 or resid 350 REMARK 3 through 354)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : 1.52839717372 REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (chain "A" and resid 401) REMARK 3 SELECTION : (chain "C" and resid 401) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : 0.253287830809 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7CCY 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_1300017401. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-14 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 : 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 : 25907 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 48.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10200 REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.62300 REMARK 200 FOR SHELL : 2.800 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 (%): 40.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, DIAMMONIUM HYDROGEN CITRATE, REMARK 280 DITHOTHREITOL, 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 37.00550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.54850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.61850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.54850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.00550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.61850 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 MET A 18 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 PHE A 77 REMARK 465 THR A 78 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 MET C 18 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 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 79 CG CD CE NZ REMARK 470 GLU A 80 CG CD OE1 OE2 REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 LYS A 132 CG CD CE NZ REMARK 470 GLU A 209 CG CD OE1 OE2 REMARK 470 LYS A 227 CG CD CE NZ REMARK 470 GLU A 258 CG CD OE1 OE2 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 ASP A 311 CG OD1 OD2 REMARK 470 ARG C 19 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 22 CG CD NE CZ NH1 NH2 REMARK 470 LEU C 64 CG CD1 CD2 REMARK 470 ASP C 65 CG OD1 OD2 REMARK 470 THR C 66 OG1 CG2 REMARK 470 LYS C 79 CG CD CE NZ REMARK 470 GLU C 80 CG CD OE1 OE2 REMARK 470 LYS C 128 CG CD CE NZ REMARK 470 GLU C 135 CG CD OE1 OE2 REMARK 470 LYS C 140 CG CD CE NZ REMARK 470 GLU C 162 CG CD OE1 OE2 REMARK 470 ARG C 164 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 229 CG CD OE1 NE2 REMARK 470 ASP C 273 CG OD1 OD2 REMARK 470 GLN C 356 CG CD OE1 NE2 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 OE2 GLU A 117 O HOH A 501 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS C 87 CE LYS C 87 NZ 0.182 REMARK 500 LYS C 157 CE LYS C 157 NZ -0.187 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 GLU C 52 CB - CA - C ANGL. DEV. = -15.6 DEGREES REMARK 500 GLU C 52 CA - CB - CG ANGL. DEV. = 21.5 DEGREES REMARK 500 LYS C 87 CA - CB - CG ANGL. DEV. = 17.9 DEGREES REMARK 500 LYS C 87 CB - CG - CD ANGL. DEV. = -18.7 DEGREES REMARK 500 LYS C 87 CD - CE - NZ ANGL. DEV. = -27.7 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 THR A 59 -129.62 -89.53 REMARK 500 CYS A 211 100.43 -161.56 REMARK 500 SER A 262 54.01 -103.58 REMARK 500 VAL A 316 45.05 29.35 REMARK 500 THR C 66 148.17 178.18 REMARK 500 LEU C 68 39.69 -72.71 REMARK 500 THR C 145 143.58 -170.51 REMARK 500 CYS C 211 102.58 -162.18 REMARK 500 SER C 262 53.37 -104.91 REMARK 500 VAL C 316 43.44 29.92 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 residue FWL C 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide DPM C 402 and CYS C REMARK 800 261 DBREF 7CCY A 1 361 UNP P08397 HEM3_HUMAN 1 361 DBREF 7CCY 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 FWL C 401 17 HET DPM C 402 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 HETNAM FWL 3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-2-IODO-1H-PYRROL- HETNAM 2 FWL 3-YL]PROPANOIC ACID HETSYN DPM DIPYRROMETHANE COFACTOR HETSYN FWL 2-IODOPORPHOBILINOGEN FORMUL 3 DPM 2(C20 H24 N2 O8) FORMUL 4 FWL C10 H13 I N2 O4 FORMUL 6 HOH *64(H2 O) HELIX 1 AA1 SER A 28 TYR A 46 1 19 HELIX 2 AA2 GLU A 80 LYS A 87 1 8 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 GLY A 197 1 8 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 LEU A 257 1 18 HELIX 12 AB3 PRO A 324 LYS A 345 1 22 HELIX 13 AB4 GLY A 346 ALA A 354 1 9 HELIX 14 AB5 SER C 28 TYR C 46 1 19 HELIX 15 AB6 THR C 78 LYS C 87 1 10 HELIX 16 AB7 LYS C 98 LEU C 100 5 3 HELIX 17 AB8 PRO C 127 VAL C 130 5 4 HELIX 18 AB9 SER C 147 PHE C 158 1 12 HELIX 19 AC1 ASN C 169 GLN C 180 1 12 HELIX 20 AC2 THR C 190 GLY C 197 1 8 HELIX 21 AC3 TRP C 198 VAL C 202 5 5 HELIX 22 AC4 ASP C 228 GLY C 236 1 9 HELIX 23 AC5 VAL C 237 HIS C 239 5 3 HELIX 24 AC6 ASP C 240 LEU C 257 1 18 HELIX 25 AC7 PRO C 324 LYS C 345 1 22 HELIX 26 AC8 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 ALA A 112 O VAL A 222 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 PHE C 51 MET C 56 0 SHEET 2 AA4 5 ILE C 21 ARG C 26 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 ARG C 164 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 GLU C 293 N GLY C 280 LINK SG CYS A 261 CHA DPM A 401 1555 1555 1.77 LINK SG CYS C 261 CHA DPM C 402 1555 1555 1.77 SITE 1 AC1 16 SER A 96 LYS A 98 ASP A 99 SER A 146 SITE 2 AC1 16 SER A 147 ARG A 149 ARG A 150 ARG A 173 SITE 3 AC1 16 ALA A 189 ARG A 195 GLY A 218 CYS A 261 SITE 4 AC1 16 HOH A 503 HOH A 504 HOH A 507 HOH A 523 SITE 1 AC2 12 ARG C 26 SER C 28 GLN C 34 PHE C 77 SITE 2 AC2 12 SER C 96 ASP C 99 ARG C 167 GLY C 168 SITE 3 AC2 12 ASN C 169 LEU C 170 ARG C 173 DPM C 402 SITE 1 AC3 18 SER C 96 LYS C 98 ASP C 99 THR C 145 SITE 2 AC3 18 SER C 146 SER C 147 ARG C 149 ARG C 150 SITE 3 AC3 18 ARG C 173 LEU C 188 ALA C 189 GLY C 218 SITE 4 AC3 18 GLY C 260 SER C 262 VAL C 263 FWL C 401 SITE 5 AC3 18 HOH C 509 HOH C 519 CRYST1 74.011 81.237 109.097 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 0.013512 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012310 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009166 0.00000 MTRIX1 1 0.999988 -0.004013 -0.002728 -31.82894 1 MTRIX2 1 0.004048 0.999910 0.012784 0.55140 1 MTRIX3 1 0.002677 -0.012795 0.999915 18.52929 1 MTRIX1 2 0.999950 0.002629 -0.009607 -31.93691 1 MTRIX2 2 -0.001947 0.997519 0.070366 1.47106 1 MTRIX3 2 0.009768 -0.070344 0.997475 18.20039 1