PDB Short entry for 1PV8 HEADER LYASE 26-JUN-03 1PV8 TITLE CRYSTAL STRUCTURE OF A LOW ACTIVITY F12L MUTANT OF HUMAN TITLE 2 PORPHOBILINOGEN SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DELTA-AMINOLEVULINIC ACID DEHYDRATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PORPHOBILINOGEN SYNTHASE, ALADH; COMPND 5 EC: 4.2.1.24; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ALAD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PORPHOBILINOGEN SYNTHASE, TETRAPYRROLE BIOSYNTHESIS, REACTION KEYWDS 2 INTERMEDIATE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR S.BREINIG,J.KERVINEN,L.STITH,A.S.WASSON,R.FAIRMAN,A.WLODAWER, AUTHOR 2 A.ZDANOV,E.K.JAFFE REVDAT 7 16-AUG-23 1PV8 1 REMARK REVDAT 6 27-OCT-21 1PV8 1 REMARK SEQADV LINK REVDAT 5 13-JUL-11 1PV8 1 VERSN REVDAT 4 02-JUN-10 1PV8 1 TITLE REVDAT 3 24-FEB-09 1PV8 1 VERSN REVDAT 2 16-SEP-03 1PV8 1 REMARK REVDAT 1 09-SEP-03 1PV8 0 JRNL AUTH S.BREINIG,J.KERVINEN,L.STITH,A.S.WASSON,R.FAIRMAN, JRNL AUTH 2 A.WLODAWER,A.ZDANOV,E.K.JAFFE JRNL TITL CONTROL OF TETRAPYRROLE BIOSYNTHESIS BY ALTERNATE QUATERNARY JRNL TITL 2 FORMS OF PORPHOBILINOGEN SYNTHASE. JRNL REF NAT.STRUCT.BIOL. V. 10 757 2003 JRNL REFN ISSN 1072-8368 JRNL PMID 12897770 JRNL DOI 10.1038/NSB963 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 198949.120 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 33434 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3327 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4003 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE : 0.3830 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 459 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4238 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 241 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.87000 REMARK 3 B22 (A**2) : -3.87000 REMARK 3 B33 (A**2) : 7.73000 REMARK 3 B12 (A**2) : 4.32000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.25 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.37 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 2.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.200 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 22.880; 4.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 20.740; 5.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 25.550; 4.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 24.180; 5.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.41 REMARK 3 BSOL : 86.59 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : LIGANDS.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : IONS.TOP REMARK 3 TOPOLOGY FILE 4 : LIGANDS.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PV8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000019599. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC OPTICS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34615 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: CNS REMARK 200 STARTING MODEL: 1E51 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM BTP, 10MM BETA-MERCAPTOETHANOL, REMARK 280 10UM ZNCL2, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 76.59500 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 76.59500 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 76.59500 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: THERE IS A DIMER IN THE ASYMMETRIC UNIT. BIOLOGICALLY REMARK 300 MEANINGFUL AGGREGATE IS HEXAMER MADE BY CRYSTALLOGRAPHIC 6(3) AXIS. 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 20390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 61080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -275.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 134.35650 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 77.57076 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 155.14152 REMARK 350 BIOMT3 3 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 GLN A 2 REMARK 465 PRO A 3 REMARK 465 GLN A 4 REMARK 465 SER A 5 REMARK 465 VAL A 6 REMARK 465 LEU A 7 REMARK 465 HIS A 8 REMARK 465 SER A 9 REMARK 465 GLY A 10 REMARK 465 SER A 83 REMARK 465 ARG A 84 REMARK 465 VAL A 85 REMARK 465 PRO A 86 REMARK 465 LYS A 87 REMARK 465 ASP A 88 REMARK 465 GLU A 89 REMARK 465 ARG A 90 REMARK 465 GLY A 91 REMARK 465 SER A 92 REMARK 465 ALA A 93 REMARK 465 ALA A 94 REMARK 465 ASP A 95 REMARK 465 SER A 96 REMARK 465 PRO A 125 REMARK 465 TYR A 126 REMARK 465 THR A 127 REMARK 465 SER A 128 REMARK 465 HIS A 129 REMARK 465 GLY A 130 REMARK 465 HIS A 131 REMARK 465 CYS A 132 REMARK 465 GLY A 133 REMARK 465 LEU A 134 REMARK 465 LEU A 135 REMARK 465 SER A 136 REMARK 465 GLU A 137 REMARK 465 ASN A 138 REMARK 465 GLY A 139 REMARK 465 MET A 170 REMARK 465 MET A 171 REMARK 465 LYS A 213 REMARK 465 SER A 214 REMARK 465 SER A 215 REMARK 465 PRO A 216 REMARK 465 ALA A 217 REMARK 465 PHE A 218 REMARK 465 GLY A 219 REMARK 465 ASP A 220 REMARK 465 ARG A 221 REMARK 465 ARG A 222 REMARK 465 CYS A 223 REMARK 465 TYR A 224 REMARK 465 GLN A 225 REMARK 465 MET B 1 REMARK 465 GLN B 2 REMARK 465 SER B 83 REMARK 465 ARG B 84 REMARK 465 VAL B 85 REMARK 465 PRO B 86 REMARK 465 LYS B 87 REMARK 465 ASP B 88 REMARK 465 GLU B 89 REMARK 465 ARG B 90 REMARK 465 GLY B 91 REMARK 465 SER B 92 REMARK 465 ALA B 93 REMARK 465 ALA B 94 REMARK 465 ASP B 95 REMARK 465 SER B 96 REMARK 465 LEU B 123 REMARK 465 CYS B 124 REMARK 465 PRO B 125 REMARK 465 TYR B 126 REMARK 465 THR B 127 REMARK 465 SER B 128 REMARK 465 HIS B 129 REMARK 465 GLY B 130 REMARK 465 HIS B 131 REMARK 465 CYS B 132 REMARK 465 GLY B 133 REMARK 465 LEU B 134 REMARK 465 LEU B 135 REMARK 465 SER B 136 REMARK 465 GLU B 137 REMARK 465 ASN B 138 REMARK 465 GLY B 139 REMARK 465 MET B 170 REMARK 465 MET B 171 REMARK 465 LYS B 213 REMARK 465 SER B 214 REMARK 465 SER B 215 REMARK 465 PRO B 216 REMARK 465 ALA B 217 REMARK 465 PHE B 218 REMARK 465 GLY B 219 REMARK 465 ASP B 220 REMARK 465 ARG B 221 REMARK 465 ARG B 222 REMARK 465 CYS B 223 REMARK 465 TYR B 224 REMARK 465 GLN B 225 REMARK 465 GLU B 329 REMARK 465 GLU B 330 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 TYR A 11 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 142 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 145 CG CD OE1 OE2 REMARK 470 LYS A 159 CG CD CE NZ REMARK 470 ARG A 174 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 330 CG CD OE1 OE2 REMARK 470 GLN B 4 CG CD OE1 NE2 REMARK 470 ARG B 55 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 142 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 145 CG CD OE1 OE2 REMARK 470 LYS B 159 CG CD CE NZ REMARK 470 ASP B 169 CG OD1 OD2 REMARK 470 ARG B 209 CG CD NE CZ NH1 NH2 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 O HOH B 614 O HOH B 645 2.14 REMARK 500 O HOH A 654 O HOH A 676 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 PRO A 41 C - N - CA ANGL. DEV. = 9.8 DEGREES REMARK 500 PRO B 207 C - N - CA ANGL. DEV. = 9.6 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 PRO A 41 -37.09 -38.04 REMARK 500 LEU A 73 127.11 -35.75 REMARK 500 VAL A 81 75.99 -118.02 REMARK 500 ARG A 149 31.81 -84.33 REMARK 500 LEU A 150 -32.97 -149.01 REMARK 500 HIS A 185 30.58 -75.52 REMARK 500 ALA A 211 40.26 -55.24 REMARK 500 PRO A 253 -173.89 -64.57 REMARK 500 GLU A 329 -62.87 -97.03 REMARK 500 PRO B 41 -15.54 -37.45 REMARK 500 LEU B 50 75.43 -114.30 REMARK 500 PRO B 51 122.20 -38.06 REMARK 500 SER B 168 63.51 -109.55 REMARK 500 HIS B 185 31.77 -84.70 REMARK 500 SER B 197 -74.22 -41.15 REMARK 500 ALA B 230 62.49 -68.22 REMARK 500 PRO B 253 -179.53 -65.11 REMARK 500 LEU B 327 45.10 -82.92 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 TYR B 257 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 THE PORPHOBILINOGEN INTERMEDIATE PB1 IS BOUND REMARK 600 TO THE ENZYME ACTIVE SITE AT LYS252 AND LYS199. REMARK 600 THE LINK BETWEEN THE C5 ATOM OF PB1 AND THE NZ REMARK 600 ATOM OF LYS199 IS A DOUBLE BOND. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB1 A 350 DBREF 1PV8 A 1 330 UNP P13716 HEM2_HUMAN 1 330 DBREF 1PV8 B 1 330 UNP P13716 HEM2_HUMAN 1 330 SEQADV 1PV8 LEU A 12 UNP P13716 PHE 12 ENGINEERED MUTATION SEQADV 1PV8 LEU B 12 UNP P13716 PHE 12 ENGINEERED MUTATION SEQRES 1 A 330 MET GLN PRO GLN SER VAL LEU HIS SER GLY TYR LEU HIS SEQRES 2 A 330 PRO LEU LEU ARG ALA TRP GLN THR ALA THR THR THR LEU SEQRES 3 A 330 ASN ALA SER ASN LEU ILE TYR PRO ILE PHE VAL THR ASP SEQRES 4 A 330 VAL PRO ASP ASP ILE GLN PRO ILE THR SER LEU PRO GLY SEQRES 5 A 330 VAL ALA ARG TYR GLY VAL LYS ARG LEU GLU GLU MET LEU SEQRES 6 A 330 ARG PRO LEU VAL GLU GLU GLY LEU ARG CYS VAL LEU ILE SEQRES 7 A 330 PHE GLY VAL PRO SER ARG VAL PRO LYS ASP GLU ARG GLY SEQRES 8 A 330 SER ALA ALA ASP SER GLU GLU SER PRO ALA ILE GLU ALA SEQRES 9 A 330 ILE HIS LEU LEU ARG LYS THR PHE PRO ASN LEU LEU VAL SEQRES 10 A 330 ALA CYS ASP VAL CYS LEU CYS PRO TYR THR SER HIS GLY SEQRES 11 A 330 HIS CYS GLY LEU LEU SER GLU ASN GLY ALA PHE ARG ALA SEQRES 12 A 330 GLU GLU SER ARG GLN ARG LEU ALA GLU VAL ALA LEU ALA SEQRES 13 A 330 TYR ALA LYS ALA GLY CYS GLN VAL VAL ALA PRO SER ASP SEQRES 14 A 330 MET MET ASP GLY ARG VAL GLU ALA ILE LYS GLU ALA LEU SEQRES 15 A 330 MET ALA HIS GLY LEU GLY ASN ARG VAL SER VAL MET SER SEQRES 16 A 330 TYR SER ALA LYS PHE ALA SER CYS PHE TYR GLY PRO PHE SEQRES 17 A 330 ARG ASP ALA ALA LYS SER SER PRO ALA PHE GLY ASP ARG SEQRES 18 A 330 ARG CYS TYR GLN LEU PRO PRO GLY ALA ARG GLY LEU ALA SEQRES 19 A 330 LEU ARG ALA VAL ASP ARG ASP VAL ARG GLU GLY ALA ASP SEQRES 20 A 330 MET LEU MET VAL LYS PRO GLY MET PRO TYR LEU ASP ILE SEQRES 21 A 330 VAL ARG GLU VAL LYS ASP LYS HIS PRO ASP LEU PRO LEU SEQRES 22 A 330 ALA VAL TYR HIS VAL SER GLY GLU PHE ALA MET LEU TRP SEQRES 23 A 330 HIS GLY ALA GLN ALA GLY ALA PHE ASP LEU LYS ALA ALA SEQRES 24 A 330 VAL LEU GLU ALA MET THR ALA PHE ARG ARG ALA GLY ALA SEQRES 25 A 330 ASP ILE ILE ILE THR TYR TYR THR PRO GLN LEU LEU GLN SEQRES 26 A 330 TRP LEU LYS GLU GLU SEQRES 1 B 330 MET GLN PRO GLN SER VAL LEU HIS SER GLY TYR LEU HIS SEQRES 2 B 330 PRO LEU LEU ARG ALA TRP GLN THR ALA THR THR THR LEU SEQRES 3 B 330 ASN ALA SER ASN LEU ILE TYR PRO ILE PHE VAL THR ASP SEQRES 4 B 330 VAL PRO ASP ASP ILE GLN PRO ILE THR SER LEU PRO GLY SEQRES 5 B 330 VAL ALA ARG TYR GLY VAL LYS ARG LEU GLU GLU MET LEU SEQRES 6 B 330 ARG PRO LEU VAL GLU GLU GLY LEU ARG CYS VAL LEU ILE SEQRES 7 B 330 PHE GLY VAL PRO SER ARG VAL PRO LYS ASP GLU ARG GLY SEQRES 8 B 330 SER ALA ALA ASP SER GLU GLU SER PRO ALA ILE GLU ALA SEQRES 9 B 330 ILE HIS LEU LEU ARG LYS THR PHE PRO ASN LEU LEU VAL SEQRES 10 B 330 ALA CYS ASP VAL CYS LEU CYS PRO TYR THR SER HIS GLY SEQRES 11 B 330 HIS CYS GLY LEU LEU SER GLU ASN GLY ALA PHE ARG ALA SEQRES 12 B 330 GLU GLU SER ARG GLN ARG LEU ALA GLU VAL ALA LEU ALA SEQRES 13 B 330 TYR ALA LYS ALA GLY CYS GLN VAL VAL ALA PRO SER ASP SEQRES 14 B 330 MET MET ASP GLY ARG VAL GLU ALA ILE LYS GLU ALA LEU SEQRES 15 B 330 MET ALA HIS GLY LEU GLY ASN ARG VAL SER VAL MET SER SEQRES 16 B 330 TYR SER ALA LYS PHE ALA SER CYS PHE TYR GLY PRO PHE SEQRES 17 B 330 ARG ASP ALA ALA LYS SER SER PRO ALA PHE GLY ASP ARG SEQRES 18 B 330 ARG CYS TYR GLN LEU PRO PRO GLY ALA ARG GLY LEU ALA SEQRES 19 B 330 LEU ARG ALA VAL ASP ARG ASP VAL ARG GLU GLY ALA ASP SEQRES 20 B 330 MET LEU MET VAL LYS PRO GLY MET PRO TYR LEU ASP ILE SEQRES 21 B 330 VAL ARG GLU VAL LYS ASP LYS HIS PRO ASP LEU PRO LEU SEQRES 22 B 330 ALA VAL TYR HIS VAL SER GLY GLU PHE ALA MET LEU TRP SEQRES 23 B 330 HIS GLY ALA GLN ALA GLY ALA PHE ASP LEU LYS ALA ALA SEQRES 24 B 330 VAL LEU GLU ALA MET THR ALA PHE ARG ARG ALA GLY ALA SEQRES 25 B 330 ASP ILE ILE ILE THR TYR TYR THR PRO GLN LEU LEU GLN SEQRES 26 B 330 TRP LEU LYS GLU GLU HET ZN A 401 1 HET PB1 A 350 16 HET ZN B 401 1 HETNAM ZN ZINC ION HETNAM PB1 3-(2-AMINOETHYL)-4-(AMINOMETHYL)HEPTANEDIOIC ACID FORMUL 3 ZN 2(ZN 2+) FORMUL 4 PB1 C10 H20 N2 O4 FORMUL 6 HOH *241(H2 O) HELIX 1 1 HIS A 13 THR A 21 1 9 HELIX 2 2 ASN A 27 SER A 29 5 3 HELIX 3 3 GLY A 57 GLY A 72 1 16 HELIX 4 4 SER A 99 PHE A 112 1 14 HELIX 5 5 ALA A 140 GLY A 161 1 22 HELIX 6 6 GLY A 173 HIS A 185 1 13 HELIX 7 7 SER A 202 PHE A 204 5 3 HELIX 8 8 TYR A 205 ALA A 211 1 7 HELIX 9 9 ALA A 230 GLU A 244 1 15 HELIX 10 10 GLY A 254 PRO A 256 5 3 HELIX 11 11 TYR A 257 HIS A 268 1 12 HELIX 12 12 VAL A 278 ALA A 291 1 14 HELIX 13 13 ASP A 295 GLY A 311 1 17 HELIX 14 14 TYR A 319 LEU A 327 1 9 HELIX 15 15 HIS B 13 ALA B 22 1 10 HELIX 16 16 ASN B 27 SER B 29 5 3 HELIX 17 17 ARG B 60 GLU B 71 1 12 HELIX 18 18 SER B 99 PHE B 112 1 14 HELIX 19 19 ALA B 140 ALA B 160 1 21 HELIX 20 20 GLY B 173 HIS B 185 1 13 HELIX 21 21 SER B 202 GLY B 206 5 5 HELIX 22 22 PHE B 208 ALA B 212 5 5 HELIX 23 23 ALA B 230 GLU B 244 1 15 HELIX 24 24 GLY B 254 PRO B 256 5 3 HELIX 25 25 TYR B 257 HIS B 268 1 12 HELIX 26 26 VAL B 278 ALA B 291 1 14 HELIX 27 27 ASP B 295 GLY B 311 1 17 HELIX 28 28 TYR B 319 LEU B 327 1 9 SHEET 1 A 9 SER A 192 VAL A 193 0 SHEET 2 A 9 VAL A 164 PRO A 167 1 N VAL A 165 O SER A 192 SHEET 3 A 9 LEU A 116 VAL A 121 1 N CYS A 119 O ALA A 166 SHEET 4 A 9 CYS A 75 GLY A 80 1 N ILE A 78 O ASP A 120 SHEET 5 A 9 LEU A 31 VAL A 37 1 N VAL A 37 O PHE A 79 SHEET 6 A 9 ILE A 314 THR A 317 1 O ILE A 315 N ILE A 32 SHEET 7 A 9 LEU A 273 HIS A 277 1 N HIS A 277 O ILE A 316 SHEET 8 A 9 LEU A 249 LYS A 252 1 N LEU A 249 O ALA A 274 SHEET 9 A 9 ALA A 198 LYS A 199 1 N ALA A 198 O MET A 250 SHEET 1 B 2 ILE A 44 PRO A 46 0 SHEET 2 B 2 ALA A 54 TYR A 56 -1 O ARG A 55 N GLN A 45 SHEET 1 C 9 LEU B 31 VAL B 37 0 SHEET 2 C 9 CYS B 75 GLY B 80 1 O LEU B 77 N ILE B 35 SHEET 3 C 9 LEU B 116 VAL B 121 1 O ALA B 118 N VAL B 76 SHEET 4 C 9 VAL B 164 PRO B 167 1 O ALA B 166 N VAL B 121 SHEET 5 C 9 SER B 192 LYS B 199 1 O MET B 194 N VAL B 165 SHEET 6 C 9 MET B 248 LYS B 252 1 O LYS B 252 N ALA B 198 SHEET 7 C 9 LEU B 273 HIS B 277 1 O ALA B 274 N LEU B 249 SHEET 8 C 9 ILE B 314 THR B 317 1 O ILE B 316 N HIS B 277 SHEET 9 C 9 LEU B 31 VAL B 37 1 N ILE B 32 O ILE B 315 SHEET 1 D 2 ILE B 44 PRO B 46 0 SHEET 2 D 2 ALA B 54 TYR B 56 -1 O ARG B 55 N GLN B 45 LINK NZ LYS A 199 C5 PB1 A 350 1555 1555 1.29 LINK NZ LYS A 252 C3 PB1 A 350 1555 1555 1.45 CISPEP 1 LYS A 252 PRO A 253 0 -0.64 CISPEP 2 LYS B 252 PRO B 253 0 0.19 SITE 1 AC1 3 CYS A 122 CYS A 124 SER A 168 SITE 1 AC2 1 SER B 168 SITE 1 AC3 11 PHE A 79 SER A 168 TYR A 196 LYS A 199 SITE 2 AC3 11 TYR A 205 PHE A 208 ARG A 209 LYS A 252 SITE 3 AC3 11 SER A 279 TYR A 318 HOH A 565 CRYST1 89.571 89.571 153.190 90.00 90.00 120.00 P 63 12 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 0.011164 0.006446 0.000000 0.00000 SCALE2 0.000000 0.012891 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006528 0.00000