PDB Short entry for 1E51 HEADER LYASE 13-JUL-00 1E51 TITLE CRYSTAL STRUCTURE OF NATIVE HUMAN ERYTHROCYTE 5-AMINOLAEVULINIC ACID TITLE 2 DEHYDRATASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DELTA-AMINOLEVULINIC ACID DEHYDRATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALADH, PORPHOBILINOGEN SYNTHASE, PORPHOBILINOGEN SYNTHASE, COMPND 5 ALADH; COMPND 6 EC: 4.2.1.24; COMPND 7 OTHER_DETAILS: PORPHOBILINOGEN IN ACTIVE SITE OF MONOMER A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL: ERYTHROCYTES KEYWDS DEHYDRATASE, TETRAPYRROLE BIOSYNTHESIS, TIM BARREL, PORPHOBILINOGEN KEYWDS 2 SYNTHASE, LEAD POISONING, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR N.L.MILLS-DAVIES,D.THOMPSON,J.B.COOPER,P.M.SHOOLINGIN-JORDAN REVDAT 5 13-DEC-23 1E51 1 REMARK LINK REVDAT 4 18-APR-18 1E51 1 JRNL REVDAT 3 05-FEB-14 1E51 1 HEADER COMPND KEYWDS AUTHOR REVDAT 3 2 1 REMARK VERSN MASTER REVDAT 2 24-FEB-09 1E51 1 VERSN REVDAT 1 12-JUL-01 1E51 0 JRNL AUTH N.L.MILLS-DAVIES,D.THOMPSON,J.B.COOPER,S.P.WOOD, JRNL AUTH 2 P.M.SHOOLINGIN-JORDAN JRNL TITL THE CRYSTAL STRUCTURE OF HUMAN ALA-DEHYDRATASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.83 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 18652 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) : 0.213 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 872 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.83 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.01 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2471 REMARK 3 BIN R VALUE (WORKING SET) : 0.3350 REMARK 3 BIN FREE R VALUE : 0.4210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 76 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.048 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4680 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.14000 REMARK 3 B22 (A**2) : -5.14000 REMARK 3 B33 (A**2) : 10.29000 REMARK 3 B12 (A**2) : 0.00000 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) : 0.34 REMARK 3 ESD FROM SIGMAA (A) : 0.45 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) : 0.42 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.61 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.990 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 66.63 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : PBG.PAR REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : PBG.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BREAK IN CHAIN A 137-138 DUE TO REMARK 3 DISORDER. BREAKS IN CHAIN B 89-93, 127-142 AND 213-220 DUE TO REMARK 3 DISORDER. REMARK 4 REMARK 4 1E51 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JUL-00. REMARK 100 THE DEPOSITION ID IS D_1290005011. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-98 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.20 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18652 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.832 REMARK 200 RESOLUTION RANGE LOW (A) : 54.233 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.25700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR, CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 1AW5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES, AMMONIUM SULPHATE, DIOXANE, PH REMARK 280 6.20 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 62.76500 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 100.45500 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 62.76500 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 100.45500 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 62.76500 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 100.45500 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 62.76500 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 100.45500 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 62.76500 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 100.45500 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 62.76500 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 100.45500 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 62.76500 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 100.45500 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 62.76500 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 62.76500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 100.45500 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 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 43900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 72950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -509.2 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 125.53000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 125.53000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 125.53000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 125.53000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 PORPHOBILINOGEN PRODUCT MOLECULE BOUND AT MONOMER A ACTIVE REMARK 400 SITE. SECOND STEP IN PORPHYRIN AND HEME BIOSYNTHESIS REMARK 400 DISEASE: DEFECTS IN ALAD ARE THE CAUSE OF ACUTE HEPATIC PORPHYRIA REMARK 400 CATALYTIC ACTIVITY: 2 5-AMINOLEVULINATE = PORPHOBILINOGEN + H(2)O REMARK 400 COFACTOR: ZINC REMARK 400 POLYMORPHISM: THERE ARE TWO COMMON ALLELES OF ALAD. INDIVIDUALS REMARK 400 HETEROZYGOUS OR HOMOZYGOUS FOR THE 2ND ALLELE HAVE SIGNIFICANTLY REMARK 400 HIGHER BLOOD LEAD LEVELS THAN DO 1ST ALLELE HOMOZYGOTES WHEN REMARK 400 EXPOSED TO ENVIRONMENTAL LEAD. 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 GLU A 137 REMARK 465 ASN A 138 REMARK 465 GLU A 329 REMARK 465 GLU A 330 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 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 ALA B 140 REMARK 465 PHE B 141 REMARK 465 ARG B 142 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 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 THR A 23 OG1 CG2 REMARK 470 GLN A 45 CG CD OE1 NE2 REMARK 470 SER A 49 OG REMARK 470 LYS A 59 CG CD CE NZ REMARK 470 GLU A 70 CG CD OE1 OE2 REMARK 470 ARG A 84 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 85 CG1 CG2 REMARK 470 ASP A 88 CG OD1 OD2 REMARK 470 ARG A 90 CG CD NE CZ NH1 NH2 REMARK 470 SER A 92 OG REMARK 470 SER A 96 OG REMARK 470 GLU A 97 CG CD OE1 OE2 REMARK 470 GLU A 98 CG CD OE1 OE2 REMARK 470 LYS A 110 CG CD CE NZ REMARK 470 LEU A 134 CG CD1 CD2 REMARK 470 ARG A 142 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 145 CG CD OE1 OE2 REMARK 470 SER A 146 OG REMARK 470 GLN A 148 CG CD OE1 NE2 REMARK 470 ARG A 149 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 152 CG CD OE1 OE2 REMARK 470 SER A 215 OG REMARK 470 THR B 23 OG1 CG2 REMARK 470 GLN B 45 CG CD OE1 NE2 REMARK 470 SER B 49 OG REMARK 470 LYS B 59 CG CD CE NZ REMARK 470 GLU B 70 CG CD OE1 OE2 REMARK 470 ARG B 84 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 85 CG1 CG2 REMARK 470 PRO B 86 CG CD REMARK 470 LYS B 87 CG CD CE NZ REMARK 470 ASP B 88 CG OD1 OD2 REMARK 470 ASP B 95 CG OD1 OD2 REMARK 470 GLU B 97 CG CD OE1 OE2 REMARK 470 GLU B 98 CG CD OE1 OE2 REMARK 470 LYS B 110 CG CD CE NZ REMARK 470 GLU B 145 CG CD OE1 OE2 REMARK 470 SER B 146 OG REMARK 470 GLN B 148 CG CD OE1 NE2 REMARK 470 ARG B 149 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 152 CG CD OE1 OE2 REMARK 470 ARG B 209 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 221 CG CD NE CZ NH1 NH2 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 B 51 C - N - CA ANGL. DEV. = 9.2 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 3 -174.41 -58.24 REMARK 500 GLN A 4 -27.80 63.79 REMARK 500 TYR A 11 -93.90 -124.02 REMARK 500 PHE A 12 -7.60 56.09 REMARK 500 THR A 23 3.48 83.08 REMARK 500 ALA A 28 -49.75 -24.85 REMARK 500 VAL A 40 98.19 -45.60 REMARK 500 ILE A 44 39.67 -171.28 REMARK 500 LYS A 59 5.77 -59.67 REMARK 500 ARG A 60 27.84 -153.40 REMARK 500 PRO A 82 93.71 -69.03 REMARK 500 ASP A 88 -176.99 -69.08 REMARK 500 SER A 92 4.88 -60.67 REMARK 500 SER A 96 -128.03 -76.02 REMARK 500 GLU A 97 -124.19 -58.56 REMARK 500 CYS A 122 -169.68 -164.82 REMARK 500 CYS A 132 47.07 -91.44 REMARK 500 ALA A 140 -124.89 -95.71 REMARK 500 ALA A 143 -79.96 -41.98 REMARK 500 TYR A 196 65.30 -68.55 REMARK 500 LYS A 213 3.96 52.83 REMARK 500 PRO A 216 96.04 -60.21 REMARK 500 PHE A 218 -73.11 -91.75 REMARK 500 TYR A 224 -25.99 -142.82 REMARK 500 PRO A 228 -48.74 -29.65 REMARK 500 PRO A 253 -174.45 -57.96 REMARK 500 PRO A 256 2.72 -63.23 REMARK 500 TRP A 326 -9.62 -54.88 REMARK 500 LEU A 327 38.70 -95.75 REMARK 500 PRO B 3 -177.19 -57.68 REMARK 500 GLN B 4 -19.55 58.29 REMARK 500 TYR B 11 -107.08 -106.77 REMARK 500 PHE B 12 -2.19 66.69 REMARK 500 ALA B 22 173.32 -57.29 REMARK 500 THR B 23 -19.94 86.23 REMARK 500 ALA B 28 -65.88 9.48 REMARK 500 ASP B 39 -77.52 -73.83 REMARK 500 VAL B 40 99.75 -39.08 REMARK 500 ILE B 44 52.03 -168.96 REMARK 500 PRO B 51 129.19 -38.38 REMARK 500 SER B 83 -18.03 -166.56 REMARK 500 LYS B 87 86.09 90.03 REMARK 500 SER B 96 57.52 -164.61 REMARK 500 GLU B 97 -74.02 -107.57 REMARK 500 SER B 99 150.16 -49.46 REMARK 500 PRO B 125 -116.04 -68.48 REMARK 500 PRO B 228 -56.09 -27.17 REMARK 500 PRO B 253 -169.05 -64.98 REMARK 500 PHE B 294 152.35 169.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 122 SG REMARK 620 2 CYS A 132 SG 112.0 REMARK 620 3 PBG A 500 N1 106.8 127.6 REMARK 620 N 1 2 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PBG A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AW5 RELATED DB: PDB REMARK 900 5-AMINOLEVULINATE DEHYDRATASE FROM SACCHAROMYCES CEREVISIAE DBREF 1E51 A 1 330 UNP P13716 HEM2_HUMAN 1 330 DBREF 1E51 B 1 330 UNP P13716 HEM2_HUMAN 1 330 SEQRES 1 A 330 MET GLN PRO GLN SER VAL LEU HIS SER GLY TYR PHE 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 PHE 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 PBG A 500 16 HET ZN A 501 1 HET SO4 A 502 5 HET SO4 B 503 5 HETNAM PBG 3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROL-3- HETNAM 2 PBG YL]PROPANOIC ACID HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETSYN PBG 2-AMINOMETHYLPYRROL-3-ACETIC ACID 4-PROPIONIC ACID; HETSYN 2 PBG PORPHOBILINOGEN; 5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H- HETSYN 3 PBG PYRROLE-3-PROPANOIC ACID FORMUL 3 PBG C10 H14 N2 O4 FORMUL 4 ZN ZN 2+ FORMUL 5 SO4 2(O4 S 2-) HELIX 1 1 LEU A 7 TYR A 11 5 5 HELIX 2 2 HIS A 13 ALA A 22 1 10 HELIX 3 3 ASN A 27 SER A 29 5 3 HELIX 4 4 ARG A 60 GLU A 71 1 12 HELIX 5 5 SER A 99 PHE A 112 1 14 HELIX 6 6 ARG A 142 ALA A 160 1 19 HELIX 7 7 GLY A 173 HIS A 185 1 13 HELIX 8 8 TYR A 205 LYS A 213 1 9 HELIX 9 9 ASP A 220 TYR A 224 5 5 HELIX 10 10 ALA A 230 GLU A 244 1 15 HELIX 11 11 GLY A 254 PRO A 256 5 3 HELIX 12 12 TYR A 257 HIS A 268 1 12 HELIX 13 13 VAL A 278 ALA A 291 1 14 HELIX 14 14 ASP A 295 GLY A 311 1 17 HELIX 15 15 TYR A 319 LEU A 327 1 9 HELIX 16 16 LEU B 7 TYR B 11 5 5 HELIX 17 17 HIS B 13 GLN B 20 1 8 HELIX 18 18 ASN B 27 SER B 29 5 3 HELIX 19 19 GLY B 57 GLU B 71 1 15 HELIX 20 20 SER B 99 PHE B 112 1 14 HELIX 21 21 GLU B 145 ALA B 160 1 16 HELIX 22 22 GLY B 173 HIS B 185 1 13 HELIX 23 23 TYR B 205 ALA B 212 1 8 HELIX 24 24 ALA B 230 GLU B 244 1 15 HELIX 25 25 GLY B 254 PRO B 256 5 3 HELIX 26 26 TYR B 257 HIS B 268 1 12 HELIX 27 27 VAL B 278 GLN B 290 1 13 HELIX 28 28 ASP B 295 ALA B 310 1 16 HELIX 29 29 TYR B 319 LEU B 327 1 9 SHEET 1 A 5 ARG A 55 GLY A 57 0 SHEET 2 A 5 TYR A 33 THR A 38 1 N PHE A 36 O TYR A 56 SHEET 3 A 5 CYS A 75 VAL A 81 1 N LEU A 77 O TYR A 33 SHEET 4 A 5 LEU A 116 VAL A 121 1 N LEU A 116 O VAL A 76 SHEET 5 A 5 VAL A 164 PRO A 167 1 N VAL A 164 O CYS A 119 SHEET 1 B 3 MET A 248 VAL A 251 0 SHEET 2 B 3 PRO A 272 HIS A 277 1 N PRO A 272 O LEU A 249 SHEET 3 B 3 ILE A 314 THR A 317 1 N ILE A 314 O VAL A 275 SHEET 1 C 4 TYR B 33 THR B 38 0 SHEET 2 C 4 CYS B 75 VAL B 81 1 N LEU B 77 O TYR B 33 SHEET 3 C 4 LEU B 116 VAL B 121 1 N LEU B 116 O VAL B 76 SHEET 4 C 4 VAL B 164 PRO B 167 1 N VAL B 164 O CYS B 119 SHEET 1 D 3 MET B 248 VAL B 251 0 SHEET 2 D 3 PRO B 272 HIS B 277 1 N PRO B 272 O LEU B 249 SHEET 3 D 3 ILE B 314 THR B 317 1 N ILE B 314 O VAL B 275 LINK NZ LYS A 252 C3A PBG A 500 1555 1555 1.98 LINK NZ LYS A 252 C4A PBG A 500 1555 1555 1.63 LINK SG CYS A 122 ZN ZN A 501 1555 1555 2.61 LINK SG CYS A 132 ZN ZN A 501 1555 1555 2.73 LINK N1 PBG A 500 ZN ZN A 501 1555 1555 2.67 CISPEP 1 LYS A 252 PRO A 253 0 -4.53 CISPEP 2 LYS B 252 PRO B 253 0 0.08 SITE 1 AC1 4 CYS A 122 CYS A 124 CYS A 132 PBG A 500 SITE 1 AC2 2 ARG A 17 ARG B 222 SITE 1 AC3 2 PRO B 14 ARG B 17 SITE 1 AC4 13 CYS A 124 SER A 168 LYS A 199 TYR A 205 SITE 2 AC4 13 PHE A 208 ARG A 209 ARG A 221 GLN A 225 SITE 3 AC4 13 LYS A 252 VAL A 278 SER A 279 TYR A 318 SITE 4 AC4 13 ZN A 501 CRYST1 125.530 125.530 200.910 90.00 90.00 90.00 I 4 2 2 32 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 0.007966 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007966 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004977 0.00000