HEADER DEHYDRATASE 21-OCT-99 1QNV TITLE YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE LEAD (PB) COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5-AMINOLAEVULINIC ACID DEHYDRATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALAD, PORPHOBILINOGEN SYNTHASE; COMPND 5 EC: 4.2.1.24; COMPND 6 OTHER_DETAILS: PB ACETATE CO-CRYSTAL SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 STRAIN: NS1(JM109/PNS1); SOURCE 6 PLASMID: PNS1 KEYWDS DEHYDRATASE, ALDOLASE, TIM BARREL, TETRAPYRROLE SYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR P.T.ERSKINE,N.M.SENIOR,M.J.WARREN,S.P.WOOD,J.B.COOPER REVDAT 4 13-DEC-23 1QNV 1 REMARK LINK REVDAT 3 22-MAY-19 1QNV 1 REMARK REVDAT 2 24-FEB-09 1QNV 1 VERSN REVDAT 1 19-OCT-00 1QNV 0 SPRSDE 19-OCT-00 1QNV 1QMK JRNL AUTH P.T.ERSKINE,E.M.H.DUKE,I.J.TICKLE,N.M.SENIOR,M.J.WARREN, JRNL AUTH 2 J.B.COOPER JRNL TITL MAD ANALYSES OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE. JRNL TITL 2 THEIR USE IN STRUCTURE DETERMINATION AND IN DEFINING THE JRNL TITL 3 METAL BINDING SITES JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 56 421 2000 JRNL REFN ISSN 0907-4449 JRNL PMID 10739915 JRNL DOI 10.1107/S0907444900000597 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CCP4 REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 13008 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.252 REMARK 3 FREE R VALUE : 0.379 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 644 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2546 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 51.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.20 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : 0.50 REMARK 3 LOW RESOLUTION CUTOFF (A) : 14.6 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.006 ; NULL REMARK 3 ANGLE DISTANCE (A) : 0.019 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.012 ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.011 ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.010 ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.026 ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QNV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1290004311. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-95 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.875 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 : AGROVATA, SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14956 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 14.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 37.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.24300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: 1AW5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AS FOR PDB ENTRY 1AW5 WITH 1MM LEAD REMARK 280 ACETATE, PH 8.00 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 51.20000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 51.20000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 85.25000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 51.20000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 51.20000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 85.25000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 51.20000 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 51.20000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 85.25000 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 51.20000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 51.20000 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 85.25000 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 51.20000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 51.20000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 85.25000 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 51.20000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 51.20000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 85.25000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 51.20000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 51.20000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 85.25000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 51.20000 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 51.20000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 85.25000 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: PQS 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 0.00000 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 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 7 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 8 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 8 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 ARG A 220 REMARK 465 ASP A 221 REMARK 465 ALA A 222 REMARK 465 ALA A 223 REMARK 465 CYS A 224 REMARK 465 SER A 225 REMARK 465 ALA A 226 REMARK 465 PRO A 227 REMARK 465 SER A 228 REMARK 465 ASN A 229 REMARK 465 GLY A 230 REMARK 465 ASP A 231 REMARK 465 ARG A 232 REMARK 465 LYS A 233 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 LEU A 60 CG CD1 CD2 REMARK 470 PHE A 219 CG CD1 CD2 CE1 CE2 CZ 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 A 2220 O HOH A 2315 1.96 REMARK 500 O HOH A 2140 O HOH A 2238 2.00 REMARK 500 O HOH A 2332 O HOH A 2333 2.02 REMARK 500 O HOH A 2132 O HOH A 2133 2.05 REMARK 500 O HOH A 2287 O HOH A 2295 2.09 REMARK 500 O HOH A 2079 O HOH A 2152 2.13 REMARK 500 O HOH A 2324 O HOH A 2339 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2011 O HOH A 2011 16554 1.17 REMARK 500 O HOH A 2227 O HOH A 2227 5555 1.31 REMARK 500 O HOH A 2028 O HOH A 2028 5555 1.98 REMARK 500 O THR A 12 NH2 ARG A 191 5555 2.06 REMARK 500 O HOH A 2129 O HOH A 2255 5555 2.13 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 CYS A 135 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 GLU A 341 C - N - CA ANGL. DEV. = 16.7 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 12 121.22 -39.06 REMARK 500 SER A 15 36.83 -91.44 REMARK 500 ASN A 39 20.30 -75.76 REMARK 500 PRO A 51 -4.71 -43.44 REMARK 500 PHE A 54 48.95 176.98 REMARK 500 ILE A 57 -141.60 -88.51 REMARK 500 ASP A 58 157.66 156.62 REMARK 500 SER A 59 -21.17 172.03 REMARK 500 LEU A 60 0.30 162.67 REMARK 500 ARG A 65 75.74 -109.80 REMARK 500 VAL A 68 -7.38 -48.75 REMARK 500 ASP A 99 -173.55 179.79 REMARK 500 PRO A 100 5.70 -69.94 REMARK 500 VAL A 101 17.23 -152.93 REMARK 500 LEU A 126 155.92 -48.77 REMARK 500 ASP A 149 57.39 29.59 REMARK 500 THR A 151 165.42 -47.95 REMARK 500 ARG A 154 -87.36 -18.19 REMARK 500 SER A 179 58.99 -104.80 REMARK 500 ASP A 180 -63.26 -104.36 REMARK 500 MET A 181 -0.66 94.93 REMARK 500 TYR A 207 57.85 -92.92 REMARK 500 ASN A 214 18.86 -68.29 REMARK 500 PRO A 239 -18.29 -45.93 REMARK 500 PRO A 264 -175.50 -61.93 REMARK 500 SER A 265 -77.48 -102.95 REMARK 500 CYS A 279 56.05 -97.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2006 DISTANCE = 7.85 ANGSTROMS REMARK 525 HOH A2007 DISTANCE = 8.84 ANGSTROMS REMARK 525 HOH A2008 DISTANCE = 10.09 ANGSTROMS REMARK 525 HOH A2009 DISTANCE = 8.62 ANGSTROMS REMARK 525 HOH A2010 DISTANCE = 8.88 ANGSTROMS REMARK 525 HOH A2014 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A2015 DISTANCE = 11.37 ANGSTROMS REMARK 525 HOH A2019 DISTANCE = 7.83 ANGSTROMS REMARK 525 HOH A2020 DISTANCE = 7.61 ANGSTROMS REMARK 525 HOH A2021 DISTANCE = 7.67 ANGSTROMS REMARK 525 HOH A2022 DISTANCE = 7.76 ANGSTROMS REMARK 525 HOH A2023 DISTANCE = 9.91 ANGSTROMS REMARK 525 HOH A2024 DISTANCE = 11.58 ANGSTROMS REMARK 525 HOH A2025 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH A2030 DISTANCE = 9.38 ANGSTROMS REMARK 525 HOH A2031 DISTANCE = 10.07 ANGSTROMS REMARK 525 HOH A2032 DISTANCE = 8.48 ANGSTROMS REMARK 525 HOH A2033 DISTANCE = 7.13 ANGSTROMS REMARK 525 HOH A2035 DISTANCE = 7.50 ANGSTROMS REMARK 525 HOH A2036 DISTANCE = 8.74 ANGSTROMS REMARK 525 HOH A2037 DISTANCE = 9.95 ANGSTROMS REMARK 525 HOH A2038 DISTANCE = 11.65 ANGSTROMS REMARK 525 HOH A2039 DISTANCE = 12.76 ANGSTROMS REMARK 525 HOH A2042 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH A2046 DISTANCE = 7.62 ANGSTROMS REMARK 525 HOH A2047 DISTANCE = 8.68 ANGSTROMS REMARK 525 HOH A2048 DISTANCE = 7.31 ANGSTROMS REMARK 525 HOH A2051 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH A2052 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A2054 DISTANCE = 8.60 ANGSTROMS REMARK 525 HOH A2055 DISTANCE = 10.59 ANGSTROMS REMARK 525 HOH A2056 DISTANCE = 9.65 ANGSTROMS REMARK 525 HOH A2057 DISTANCE = 7.44 ANGSTROMS REMARK 525 HOH A2058 DISTANCE = 7.89 ANGSTROMS REMARK 525 HOH A2061 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A2062 DISTANCE = 7.22 ANGSTROMS REMARK 525 HOH A2063 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH A2070 DISTANCE = 7.07 ANGSTROMS REMARK 525 HOH A2074 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A2076 DISTANCE = 9.42 ANGSTROMS REMARK 525 HOH A2080 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A2082 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A2083 DISTANCE = 8.39 ANGSTROMS REMARK 525 HOH A2084 DISTANCE = 8.42 ANGSTROMS REMARK 525 HOH A2086 DISTANCE = 7.82 ANGSTROMS REMARK 525 HOH A2088 DISTANCE = 11.94 ANGSTROMS REMARK 525 HOH A2089 DISTANCE = 8.86 ANGSTROMS REMARK 525 HOH A2090 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH A2091 DISTANCE = 7.09 ANGSTROMS REMARK 525 HOH A2092 DISTANCE = 9.26 ANGSTROMS REMARK 525 HOH A2094 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A2098 DISTANCE = 7.39 ANGSTROMS REMARK 525 HOH A2099 DISTANCE = 7.48 ANGSTROMS REMARK 525 HOH A2100 DISTANCE = 8.04 ANGSTROMS REMARK 525 HOH A2101 DISTANCE = 10.43 ANGSTROMS REMARK 525 HOH A2102 DISTANCE = 10.81 ANGSTROMS REMARK 525 HOH A2107 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A2108 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH A2113 DISTANCE = 7.11 ANGSTROMS REMARK 525 HOH A2114 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A2115 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH A2116 DISTANCE = 7.81 ANGSTROMS REMARK 525 HOH A2117 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH A2121 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH A2122 DISTANCE = 8.87 ANGSTROMS REMARK 525 HOH A2123 DISTANCE = 9.50 ANGSTROMS REMARK 525 HOH A2124 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A2127 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A2129 DISTANCE = 7.19 ANGSTROMS REMARK 525 HOH A2138 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A2145 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A2149 DISTANCE = 7.48 ANGSTROMS REMARK 525 HOH A2154 DISTANCE = 7.69 ANGSTROMS REMARK 525 HOH A2166 DISTANCE = 7.23 ANGSTROMS REMARK 525 HOH A2167 DISTANCE = 7.75 ANGSTROMS REMARK 525 HOH A2168 DISTANCE = 7.58 ANGSTROMS REMARK 525 HOH A2179 DISTANCE = 7.57 ANGSTROMS REMARK 525 HOH A2180 DISTANCE = 7.60 ANGSTROMS REMARK 525 HOH A2187 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A2189 DISTANCE = 7.26 ANGSTROMS REMARK 525 HOH A2190 DISTANCE = 7.27 ANGSTROMS REMARK 525 HOH A2206 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A2207 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A2208 DISTANCE = 7.19 ANGSTROMS REMARK 525 HOH A2209 DISTANCE = 7.62 ANGSTROMS REMARK 525 HOH A2237 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A2239 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A2240 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A2255 DISTANCE = 7.11 ANGSTROMS 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 PB A 400 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 133 SG REMARK 620 2 CYS A 135 SG 88.2 REMARK 620 3 CYS A 143 SG 98.3 109.9 REMARK 620 4 SER A 179 O 59.3 127.4 114.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PB A 401 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 141 O REMARK 620 2 CYS A 143 SG 85.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AW5 RELATED DB: PDB REMARK 900 5-AMINOLEVULINATE DEHYDRATASE FROM SACCHAROMYCES CEREVISIAE REMARK 900 RELATED ID: 1QMK RELATED DB: PDB REMARK 900 YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE LEAD (PB) COMPLEX REMARK 900 RELATED ID: 1QML RELATED DB: PDB REMARK 900 HG COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE REMARK 900 RELATED ID: 1YLV RELATED DB: PDB REMARK 900 SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE REMARK 900 WITH LAEVULINIC ACID REMARK 900 RELATED ID: 1AML RELATED DB: PDB REMARK 900 HG COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE DBREF 1QNV A 1 342 UNP P05373 HEM2_YEAST 1 342 SEQRES 1 A 342 MET HIS THR ALA GLU PHE LEU GLU THR GLU PRO THR GLU SEQRES 2 A 342 ILE SER SER VAL LEU ALA GLY GLY TYR ASN HIS PRO LEU SEQRES 3 A 342 LEU ARG GLN TRP GLN SER GLU ARG GLN LEU THR LYS ASN SEQRES 4 A 342 MET LEU ILE PHE PRO LEU PHE ILE SER ASP ASN PRO ASP SEQRES 5 A 342 ASP PHE THR GLU ILE ASP SER LEU PRO ASN ILE ASN ARG SEQRES 6 A 342 ILE GLY VAL ASN ARG LEU LYS ASP TYR LEU LYS PRO LEU SEQRES 7 A 342 VAL ALA LYS GLY LEU ARG SER VAL ILE LEU PHE GLY VAL SEQRES 8 A 342 PRO LEU ILE PRO GLY THR LYS ASP PRO VAL GLY THR ALA SEQRES 9 A 342 ALA ASP ASP PRO ALA GLY PRO VAL ILE GLN GLY ILE LYS SEQRES 10 A 342 PHE ILE ARG GLU TYR PHE PRO GLU LEU TYR ILE ILE CYS SEQRES 11 A 342 ASP VAL CYS LEU CYS GLU TYR THR SER HIS GLY HIS CYS SEQRES 12 A 342 GLY VAL LEU TYR ASP ASP GLY THR ILE ASN ARG GLU ARG SEQRES 13 A 342 SER VAL SER ARG LEU ALA ALA VAL ALA VAL ASN TYR ALA SEQRES 14 A 342 LYS ALA GLY ALA HIS CYS VAL ALA PRO SER ASP MET ILE SEQRES 15 A 342 ASP GLY ARG ILE ARG ASP ILE LYS ARG GLY LEU ILE ASN SEQRES 16 A 342 ALA ASN LEU ALA HIS LYS THR PHE VAL LEU SER TYR ALA SEQRES 17 A 342 ALA LYS PHE SER GLY ASN LEU TYR GLY PRO PHE ARG ASP SEQRES 18 A 342 ALA ALA CYS SER ALA PRO SER ASN GLY ASP ARG LYS CYS SEQRES 19 A 342 TYR GLN LEU PRO PRO ALA GLY ARG GLY LEU ALA ARG ARG SEQRES 20 A 342 ALA LEU GLU ARG ASP MET SER GLU GLY ALA ASP GLY ILE SEQRES 21 A 342 ILE VAL LYS PRO SER THR PHE TYR LEU ASP ILE MET ARG SEQRES 22 A 342 ASP ALA SER GLU ILE CYS LYS ASP LEU PRO ILE CYS ALA SEQRES 23 A 342 TYR HIS VAL SER GLY GLU TYR ALA MET LEU HIS ALA ALA SEQRES 24 A 342 ALA GLU LYS GLY VAL VAL ASP LEU LYS THR ILE ALA PHE SEQRES 25 A 342 GLU SER HIS GLN GLY PHE LEU ARG ALA GLY ALA ARG LEU SEQRES 26 A 342 ILE ILE THR TYR LEU ALA PRO GLU PHE LEU ASP TRP LEU SEQRES 27 A 342 ASP GLU GLU ASN HET PB A 400 1 HET PB A 401 1 HETNAM PB LEAD (II) ION FORMUL 2 PB 2(PB 2+) FORMUL 4 HOH *370(H2 O) HELIX 1 1 GLU A 13 VAL A 17 5 5 HELIX 2 2 LEU A 18 TYR A 22 5 5 HELIX 3 3 HIS A 24 GLN A 29 5 6 HELIX 4 4 THR A 37 ASN A 39 5 3 HELIX 5 5 ARG A 70 LYS A 81 1 12 HELIX 6 6 GLY A 102 ASP A 107 5 6 HELIX 7 7 VAL A 112 PHE A 123 1 12 HELIX 8 8 LEU A 134 TYR A 137 5 4 HELIX 9 9 ASN A 153 ALA A 171 1 19 HELIX 10 10 GLY A 184 ALA A 196 1 13 HELIX 11 11 GLY A 243 GLU A 255 1 13 HELIX 12 12 SER A 265 PHE A 267 5 3 HELIX 13 13 TYR A 268 CYS A 279 1 12 HELIX 14 14 VAL A 289 LYS A 302 1 14 HELIX 15 15 ASP A 306 GLY A 322 1 17 HELIX 16 16 LEU A 330 LEU A 338 1 9 SHEET 1 A 6 PHE A 54 GLU A 56 0 SHEET 2 A 6 ASN A 64 GLY A 67 -1 N ARG A 65 O THR A 55 SHEET 3 A 6 PHE A 43 SER A 48 1 N PHE A 46 O ILE A 66 SHEET 4 A 6 SER A 85 VAL A 91 1 N ILE A 87 O PHE A 43 SHEET 5 A 6 TYR A 127 VAL A 132 1 N TYR A 127 O VAL A 86 SHEET 6 A 6 CYS A 175 PRO A 178 1 N CYS A 175 O CYS A 130 SHEET 1 B 3 GLY A 259 VAL A 262 0 SHEET 2 B 3 PRO A 283 TYR A 287 1 N PRO A 283 O ILE A 260 SHEET 3 B 3 LEU A 325 ILE A 327 1 N LEU A 325 O ALA A 286 LINK SG CYS A 133 PB PB A 400 1555 1555 2.74 LINK SG CYS A 135 PB PB A 400 1555 1555 2.82 LINK O GLY A 141 PB PB A 401 1555 1555 3.48 LINK SG CYS A 143 PB PB A 400 1555 1555 2.84 LINK SG CYS A 143 PB PB A 401 1555 1555 3.47 LINK O SER A 179 PB PB A 400 1555 1555 3.38 CISPEP 1 LYS A 263 PRO A 264 0 -0.13 SITE 1 AC1 4 CYS A 133 CYS A 135 CYS A 143 SER A 179 SITE 1 AC2 3 CYS A 135 GLY A 141 CYS A 143 CRYST1 102.400 102.400 170.500 90.00 90.00 90.00 I 4 2 2 16 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 0.009766 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009766 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005865 0.00000