HEADER DEHYDRATASE 09-JUL-01 1H7O TITLE SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH TITLE 2 5-AMINOLAEVULINIC ACID AT 1.7 A RESOLUTION 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 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: SCHIFF-BASE LINK BETWEEN 5-AMINOLAEVULINIC ACID COMPND 8 SUBSTRATE (HET GROUP A1342) AND LYSINE 263 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYASE, DEHYDRATASE, ALDOLASE, TIM BARREL, TETRAPYRROLE SYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR P.T.ERSKINE,R.NEWBOLD,A.A.BRINDLEY,S.P.WOOD,P.M.SHOOLINGIN-JORDAN, AUTHOR 2 M.J.WARREN,J.B.COOPER REVDAT 7 13-DEC-23 1H7O 1 REMARK REVDAT 6 15-NOV-23 1H7O 1 LINK ATOM REVDAT 5 24-JUL-19 1H7O 1 REMARK REVDAT 4 22-MAY-19 1H7O 1 REMARK LINK REVDAT 3 24-FEB-09 1H7O 1 VERSN REVDAT 2 28-NOV-01 1H7O 1 JRNL REVDAT 1 10-JUL-01 1H7O 0 JRNL AUTH P.T.ERSKINE,R.NEWBOLD,A.A.BRINDLEY,S.P.WOOD, JRNL AUTH 2 P.M.SHOOLINGIN-JORDAN,M.J.WARREN,J.B.COOPER JRNL TITL THE X-RAY STRUCTURE OF YEAST 5-AMINOLAEVULINIC ACID JRNL TITL 2 DEHYDRATASE COMPLEXED WITH SUBSTRATE AND THREE INHIBITORS JRNL REF J.MOL.BIOL. V. 312 133 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11545591 JRNL DOI 10.1006/JMBI.2001.4947 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.259 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.353 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2284 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 45353 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.236 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.323 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1874 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 37893 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2646 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 427 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 5 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 12663 REMARK 3 NUMBER OF RESTRAINTS : 11123 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.022 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.329 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.034 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.038 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.016 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE C-TERMINAL RESIDUE WAS NOT REFINED REMARK 4 REMARK 4 1H7O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1290008302. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-98 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 : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8345 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 : 45361 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 14.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.38500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: 1YLV 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): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AS FOR 1AW5, EXCEPT ENZYME WAS NOT GEL REMARK 280 -FILTERED., 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 51.40000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 51.40000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 84.15000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 51.40000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 51.40000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 84.15000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 51.40000 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 51.40000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 84.15000 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 51.40000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 51.40000 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 84.15000 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 51.40000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 51.40000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 84.15000 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 51.40000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 51.40000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 84.15000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 51.40000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 51.40000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 84.15000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 51.40000 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 51.40000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 84.15000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2017 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2086 LIES ON A SPECIAL POSITION. 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 2009 O HOH A 2065 7555 2.14 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 ARG A 187 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 191 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 191 NE - CZ - NH2 ANGL. DEV. = -3.5 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 TYR A 22 54.45 -148.30 REMARK 500 PHE A 54 63.54 -162.47 REMARK 500 ASP A 58 -32.14 -39.04 REMARK 500 TYR A 147 -176.86 -64.82 REMARK 500 TYR A 207 80.50 -68.69 REMARK 500 ASN A 229 87.83 84.68 REMARK 500 ARG A 232 34.71 -97.45 REMARK 500 PRO A 264 -171.20 -67.95 REMARK 500 SER A 265 -77.39 -112.71 REMARK 500 CYS A 279 42.20 -106.37 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 A2007 DISTANCE = 6.76 ANGSTROMS REMARK 525 HOH A2008 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A2009 DISTANCE = 7.59 ANGSTROMS REMARK 525 HOH A2010 DISTANCE = 7.38 ANGSTROMS REMARK 525 HOH A2011 DISTANCE = 9.45 ANGSTROMS REMARK 525 HOH A2012 DISTANCE = 8.76 ANGSTROMS REMARK 525 HOH A2013 DISTANCE = 8.47 ANGSTROMS REMARK 525 HOH A2014 DISTANCE = 8.83 ANGSTROMS REMARK 525 HOH A2015 DISTANCE = 7.74 ANGSTROMS REMARK 525 HOH A2021 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A2022 DISTANCE = 7.73 ANGSTROMS REMARK 525 HOH A2024 DISTANCE = 7.89 ANGSTROMS REMARK 525 HOH A2029 DISTANCE = 8.14 ANGSTROMS REMARK 525 HOH A2030 DISTANCE = 8.34 ANGSTROMS REMARK 525 HOH A2031 DISTANCE = 8.11 ANGSTROMS REMARK 525 HOH A2032 DISTANCE = 7.84 ANGSTROMS REMARK 525 HOH A2033 DISTANCE = 7.24 ANGSTROMS REMARK 525 HOH A2034 DISTANCE = 9.75 ANGSTROMS REMARK 525 HOH A2035 DISTANCE = 9.66 ANGSTROMS REMARK 525 HOH A2044 DISTANCE = 8.09 ANGSTROMS REMARK 525 HOH A2045 DISTANCE = 7.73 ANGSTROMS REMARK 525 HOH A2048 DISTANCE = 10.80 ANGSTROMS REMARK 525 HOH A2049 DISTANCE = 7.74 ANGSTROMS REMARK 525 HOH A2050 DISTANCE = 8.30 ANGSTROMS REMARK 525 HOH A2051 DISTANCE = 8.90 ANGSTROMS REMARK 525 HOH A2052 DISTANCE = 8.04 ANGSTROMS REMARK 525 HOH A2053 DISTANCE = 9.65 ANGSTROMS REMARK 525 HOH A2054 DISTANCE = 10.24 ANGSTROMS REMARK 525 HOH A2055 DISTANCE = 11.96 ANGSTROMS REMARK 525 HOH A2056 DISTANCE = 8.71 ANGSTROMS REMARK 525 HOH A2062 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A2065 DISTANCE = 9.15 ANGSTROMS REMARK 525 HOH A2067 DISTANCE = 7.15 ANGSTROMS REMARK 525 HOH A2068 DISTANCE = 10.44 ANGSTROMS REMARK 525 HOH A2072 DISTANCE = 7.89 ANGSTROMS REMARK 525 HOH A2073 DISTANCE = 9.53 ANGSTROMS REMARK 525 HOH A2078 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH A2079 DISTANCE = 7.21 ANGSTROMS REMARK 525 HOH A2082 DISTANCE = 7.38 ANGSTROMS REMARK 525 HOH A2083 DISTANCE = 7.45 ANGSTROMS REMARK 525 HOH A2084 DISTANCE = 7.37 ANGSTROMS REMARK 525 HOH A2090 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A2091 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A2094 DISTANCE = 7.09 ANGSTROMS REMARK 525 HOH A2099 DISTANCE = 8.27 ANGSTROMS REMARK 525 HOH A2100 DISTANCE = 8.36 ANGSTROMS REMARK 525 HOH A2102 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH A2104 DISTANCE = 7.04 ANGSTROMS REMARK 525 HOH A2106 DISTANCE = 7.64 ANGSTROMS REMARK 525 HOH A2107 DISTANCE = 7.47 ANGSTROMS REMARK 525 HOH A2108 DISTANCE = 7.17 ANGSTROMS REMARK 525 HOH A2109 DISTANCE = 7.24 ANGSTROMS REMARK 525 HOH A2113 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH A2115 DISTANCE = 8.58 ANGSTROMS REMARK 525 HOH A2122 DISTANCE = 7.09 ANGSTROMS REMARK 525 HOH A2123 DISTANCE = 7.40 ANGSTROMS REMARK 525 HOH A2127 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A2128 DISTANCE = 8.21 ANGSTROMS REMARK 525 HOH A2129 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH A2131 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A2135 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A2138 DISTANCE = 6.63 ANGSTROMS REMARK 525 HOH A2160 DISTANCE = 7.59 ANGSTROMS REMARK 525 HOH A2164 DISTANCE = 7.92 ANGSTROMS REMARK 525 HOH A2165 DISTANCE = 7.36 ANGSTROMS REMARK 525 HOH A2166 DISTANCE = 6.74 ANGSTROMS REMARK 525 HOH A2167 DISTANCE = 8.48 ANGSTROMS REMARK 525 HOH A2172 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A2184 DISTANCE = 7.18 ANGSTROMS REMARK 525 HOH A2185 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A2197 DISTANCE = 7.95 ANGSTROMS REMARK 525 HOH A2213 DISTANCE = 5.89 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 ZN A1343 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 133 SG REMARK 620 2 CYS A 135 SG 114.7 REMARK 620 3 CYS A 143 SG 105.5 108.6 REMARK 620 4 HOH A2427 O 104.5 102.6 121.5 REMARK 620 N 1 2 3 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAV A1342 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: 1H7N RELATED DB: PDB REMARK 900 SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE REMARK 900 WITH LAEVULINIC ACID AT 1.6 A RESOLUTION REMARK 900 RELATED ID: 1QML RELATED DB: PDB REMARK 900 HG COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE REMARK 900 RELATED ID: 1QNV RELATED DB: PDB REMARK 900 YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE LEAD (PB) COMPLEX 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 999 REMARK 999 SEQUENCE REMARK 999 THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS DBREF 1H7O A 1 341 UNP P05373 HEM2_YEAST 1 341 SEQRES 1 A 341 MET HIS THR ALA GLU PHE LEU GLU THR GLU PRO THR GLU SEQRES 2 A 341 ILE SER SER VAL LEU ALA GLY GLY TYR ASN HIS PRO LEU SEQRES 3 A 341 LEU ARG GLN TRP GLN SER GLU ARG GLN LEU THR LYS ASN SEQRES 4 A 341 MET LEU ILE PHE PRO LEU PHE ILE SER ASP ASN PRO ASP SEQRES 5 A 341 ASP PHE THR GLU ILE ASP SER LEU PRO ASN ILE ASN ARG SEQRES 6 A 341 ILE GLY VAL ASN ARG LEU LYS ASP TYR LEU LYS PRO LEU SEQRES 7 A 341 VAL ALA LYS GLY LEU ARG SER VAL ILE LEU PHE GLY VAL SEQRES 8 A 341 PRO LEU ILE PRO GLY THR LYS ASP PRO VAL GLY THR ALA SEQRES 9 A 341 ALA ASP ASP PRO ALA GLY PRO VAL ILE GLN GLY ILE LYS SEQRES 10 A 341 PHE ILE ARG GLU TYR PHE PRO GLU LEU TYR ILE ILE CYS SEQRES 11 A 341 ASP VAL CYS LEU CYS GLU TYR THR SER HIS GLY HIS CYS SEQRES 12 A 341 GLY VAL LEU TYR ASP ASP GLY THR ILE ASN ARG GLU ARG SEQRES 13 A 341 SER VAL SER ARG LEU ALA ALA VAL ALA VAL ASN TYR ALA SEQRES 14 A 341 LYS ALA GLY ALA HIS CYS VAL ALA PRO SER ASP MET ILE SEQRES 15 A 341 ASP GLY ARG ILE ARG ASP ILE LYS ARG GLY LEU ILE ASN SEQRES 16 A 341 ALA ASN LEU ALA HIS LYS THR PHE VAL LEU SER TYR ALA SEQRES 17 A 341 ALA LYS PHE SER GLY ASN LEU TYR GLY PRO PHE ARG ASP SEQRES 18 A 341 ALA ALA CYS SER ALA PRO SER ASN GLY ASP ARG LYS CYS SEQRES 19 A 341 TYR GLN LEU PRO PRO ALA GLY ARG GLY LEU ALA ARG ARG SEQRES 20 A 341 ALA LEU GLU ARG ASP MET SER GLU GLY ALA ASP GLY ILE SEQRES 21 A 341 ILE VAL LYS PRO SER THR PHE TYR LEU ASP ILE MET ARG SEQRES 22 A 341 ASP ALA SER GLU ILE CYS LYS ASP LEU PRO ILE CYS ALA SEQRES 23 A 341 TYR HIS VAL SER GLY GLU TYR ALA MET LEU HIS ALA ALA SEQRES 24 A 341 ALA GLU LYS GLY VAL VAL ASP LEU LYS THR ILE ALA PHE SEQRES 25 A 341 GLU SER HIS GLN GLY PHE LEU ARG ALA GLY ALA ARG LEU SEQRES 26 A 341 ILE ILE THR TYR LEU ALA PRO GLU PHE LEU ASP TRP LEU SEQRES 27 A 341 ASP GLU GLU HET DAV A1342 16 HET ZN A1343 1 HETNAM DAV DELTA-AMINO VALERIC ACID HETNAM ZN ZINC ION FORMUL 2 DAV C5 H12 N O2 1+ FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *427(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 31 1 8 HELIX 4 4 THR A 37 ASN A 39 5 3 HELIX 5 5 GLY A 67 LYS A 81 1 15 HELIX 6 6 GLY A 102 ASP A 107 5 6 HELIX 7 7 GLY A 110 PHE A 123 1 14 HELIX 8 8 ASN A 153 GLY A 172 1 20 HELIX 9 9 GLY A 184 ALA A 196 1 13 HELIX 10 10 TYR A 216 ALA A 223 1 8 HELIX 11 11 GLY A 241 GLU A 255 1 15 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 ALA A 321 1 16 HELIX 16 16 LEU A 330 GLU A 341 1 12 SHEET 1 AA11 LEU A 41 SER A 48 0 SHEET 2 AA11 LEU A 325 ILE A 327 1 O ILE A 326 N ILE A 42 SHEET 3 AA11 ILE A 284 TYR A 287 1 O ALA A 286 N ILE A 327 SHEET 4 AA11 GLY A 259 LYS A 263 1 O ILE A 260 N CYS A 285 SHEET 5 AA11 PHE A 203 LYS A 210 1 O SER A 206 N ILE A 261 SHEET 6 AA11 CYS A 175 PRO A 178 1 O VAL A 176 N LEU A 205 SHEET 7 AA11 TYR A 127 VAL A 132 1 O ILE A 128 N CYS A 175 SHEET 8 AA11 SER A 85 VAL A 91 1 O VAL A 86 N ILE A 129 SHEET 9 AA11 LEU A 41 SER A 48 1 O PHE A 43 N ILE A 87 SHEET 10 AA11 LEU A 325 ILE A 327 1 O ILE A 326 N ILE A 42 SHEET 11 AA11 LEU A 41 SER A 48 1 N ILE A 42 O ILE A 326 LINK NZ ALYS A 263 CG ADAV A1342 1555 1555 1.29 LINK NZ BLYS A 263 CG BDAV A1342 1555 1555 1.30 LINK SG CYS A 133 ZN ZN A1343 1555 1555 2.25 LINK SG CYS A 135 ZN ZN A1343 1555 1555 2.27 LINK SG CYS A 143 ZN ZN A1343 1555 1555 2.26 LINK ZN ZN A1343 O HOH A2427 1555 1555 2.20 CISPEP 1 LYS A 263 PRO A 264 0 -5.36 SITE 1 AC1 4 CYS A 133 CYS A 135 CYS A 143 HOH A2427 SITE 1 AC2 12 PHE A 89 ASP A 131 SER A 179 TYR A 207 SITE 2 AC2 12 LYS A 210 TYR A 216 PHE A 219 LYS A 263 SITE 3 AC2 12 TYR A 287 VAL A 289 SER A 290 TYR A 329 CRYST1 102.800 102.800 168.300 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 0.009728 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009728 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005942 0.00000