PDB Short entry for 1W31 HEADER LYASE 11-JUL-04 1W31 TITLE YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 5-HYDROXYLAEVULINIC ACID TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DELTA-AMINOLEVULINIC ACID DEHYDRATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 5-AMINOLAEVULINIC ACID DEHYDRATASE, ALADH; COMPND 5 EC: 4.2.1.24; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: COMPLEX WITH 5-HYDROXYLAEVULINIC ACID 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DEHYDRATASE, ALDOLASE, TIM BARREL, TETRAPYRROLE SYNTHESIS, HEME KEYWDS 2 BIOSYNTHESIS, LYASE, ZINC EXPDTA X-RAY DIFFRACTION AUTHOR P.T.ERSKINE,L.COATES,R.NEWBOLD,A.A.BRINDLEY,F.STAUFFER,G.D.E.BEAVEN, AUTHOR 2 R.GILL,S.P.WOOD,M.J.WARREN,J.B.COOPER,P.M.SHOOLINGIN-JORDAN,R.NEIER REVDAT 6 13-DEC-23 1W31 1 REMARK LINK REVDAT 5 22-MAY-19 1W31 1 REMARK REVDAT 4 08-MAY-19 1W31 1 REMARK LINK REVDAT 3 13-AUG-14 1W31 1 REMARK VERSN SITE REVDAT 2 24-FEB-09 1W31 1 VERSN REVDAT 1 23-AUG-05 1W31 0 JRNL AUTH P.T.ERSKINE,L.COATES,R.NEWBOLD,A.A.BRINDLEY,F.STAUFFER, JRNL AUTH 2 G.D.E.BEAVEN,R.GILL,A.COKER,S.P.WOOD,M.J.WARREN, JRNL AUTH 3 P.M.SHOOLINGIN-JORDAN,R.NEIER,J.B.COOPER JRNL TITL STRUCTURE OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE JRNL TITL 2 COMPLEXED WITH THE INHIBITOR 5-HYDROXYLAEVULINIC ACID JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 61 1222 2005 JRNL REFN ISSN 0907-4449 JRNL PMID 16131755 JRNL DOI 10.1107/S0907444905018834 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : RESTRAIN REMARK 3 AUTHORS : MOSS,DRIESSEN,HANEEF,HOWLIN,HARRIS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : NULL 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) : 0.190 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1789 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 33934 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2637 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 269 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; 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 1W31 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1290015006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-02 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 : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.911662 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1067852 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 49.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.41900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 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: PDB ENTRY 1YLV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ENZYME CONCENTRATION 1 MG/ML, PH 7.0 - REMARK 280 8.5, BUFFER 0.2 M TRIS-HCL, PRECIPITANT PEG 6000 (<10%), 70 REMARK 280 MICROMOLAR ZINC SULPHATE, 6 MM BETA-MERCAPTOETHANOL, HANGING REMARK 280 DROPS AS FOR PDB ENTRY 1AW5 WITH 10 MM 5-HYDROXYLAEVULINIC ACID REMARK 280 IN DROP., PH 8.00, VAPOR DIFFUSION, HANGING DROP 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 51.28500 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 51.28500 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 84.19000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 51.28500 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 51.28500 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 84.19000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 51.28500 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 51.28500 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 84.19000 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 51.28500 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 51.28500 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 84.19000 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 51.28500 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 51.28500 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 84.19000 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 51.28500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 51.28500 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 84.19000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 51.28500 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 51.28500 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 84.19000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 51.28500 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 51.28500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 84.19000 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 GLU A 341 REMARK 465 ASN A 342 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 2146 O HOH A 2263 2.06 REMARK 500 O HOH A 2002 O HOH A 2004 2.08 REMARK 500 O HOH A 2038 O HOH A 2039 2.08 REMARK 500 O HOH A 2095 O HOH A 2195 2.11 REMARK 500 O HOH A 2068 O HOH A 2257 2.16 REMARK 500 O HOH A 2061 O HOH A 2063 2.18 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 2066 O HOH A 2260 5555 1.79 REMARK 500 NH2 ARG A 28 O LYS A 233 7555 2.02 REMARK 500 O HOH A 2064 O HOH A 2233 5555 2.16 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 156 CA - CB - CG ANGL. DEV. = 15.3 DEGREES REMARK 500 CYS A 234 O - C - N ANGL. DEV. = 12.5 DEGREES REMARK 500 HIS A 315 O - C - N ANGL. DEV. = 11.3 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 45.14 -149.62 REMARK 500 PHE A 54 54.23 173.73 REMARK 500 ASP A 58 -82.72 -42.95 REMARK 500 TYR A 147 -175.18 -67.70 REMARK 500 MET A 181 7.89 83.47 REMARK 500 ASN A 229 112.32 66.82 REMARK 500 PRO A 264 -174.47 -63.28 REMARK 500 SER A 265 -77.07 -109.11 REMARK 500 CYS A 279 40.97 -106.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 TYR A 235 12.27 REMARK 500 GLN A 316 -17.25 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 = 6.65 ANGSTROMS REMARK 525 HOH A2008 DISTANCE = 8.97 ANGSTROMS REMARK 525 HOH A2013 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A2014 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A2043 DISTANCE = 7.54 ANGSTROMS REMARK 525 HOH A2053 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A2072 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A2073 DISTANCE = 7.49 ANGSTROMS REMARK 525 HOH A2117 DISTANCE = 6.64 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 A 400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 133 SG REMARK 620 2 CYS A 135 SG 114.8 REMARK 620 3 CYS A 143 SG 98.8 122.5 REMARK 620 4 HOH A2269 O 102.7 97.3 119.9 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 11-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 12-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 A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SHO A 363 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: 1EB3 RELATED DB: PDB REMARK 900 YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 4,7 -DIOXOSEBACIC ACID REMARK 900 COMPLEX REMARK 900 RELATED ID: 1GJP RELATED DB: PDB REMARK 900 SCHIFF-BASE COMPLEX OF YEAST 5- AMINOLAEVULINIC ACID DEHYDRATASE REMARK 900 WITH 4- OXOSEBACIC ACID 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: 1H7O RELATED DB: PDB REMARK 900 SCHIFF-BASE COMPLEX OF YEAST 5- AMINOLAEVULINIC ACID DEHYDRATASE REMARK 900 WITH 5- AMINOLAEVULINIC ACID AT 1.7 A RESOLUTION REMARK 900 RELATED ID: 1H7P RELATED DB: PDB REMARK 900 SCHIFF-BASE COMPLEX OF YEAST 5- AMINOLAEVULINIC ACID DEHYDRATASE REMARK 900 WITH 4-KETO- 5-AMINO-HEXANOIC (KAH) AT 1.64 A RESOLUTION REMARK 900 RELATED ID: 1H7R RELATED DB: PDB REMARK 900 SCHIFF-BASE COMPLEX OF YEAST 5- AMINOLAEVULINIC ACID DEHYDRATASE REMARK 900 WITH SUCCINYLACETONE AT 2.0 A RESOLUTION. REMARK 900 RELATED ID: 1OHL RELATED DB: PDB REMARK 900 YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE PUTATIVE CYCLIC REACTION REMARK 900 INTERMEDIATE COMPLEX 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 DBREF 1W31 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 SHO A 363 16 HET ZN A 400 1 HETNAM SHO 5-HYDROXYLAEVULINIC ACID HETNAM ZN ZINC ION HETSYN SHO 5-HYDROXYPENTANOIC ACID FORMUL 2 SHO C5 H10 O3 FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *269(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 LEU A 134 TYR A 137 5 4 HELIX 9 9 ASN A 153 GLY A 172 1 20 HELIX 10 10 GLY A 184 ALA A 196 1 13 HELIX 11 11 TYR A 216 ALA A 223 1 8 HELIX 12 12 GLY A 241 GLU A 255 1 15 HELIX 13 13 SER A 265 PHE A 267 5 3 HELIX 14 14 TYR A 268 CYS A 279 1 12 HELIX 15 15 VAL A 289 LYS A 302 1 14 HELIX 16 16 ASP A 306 ALA A 321 1 16 HELIX 17 17 LEU A 330 LEU A 338 1 9 SHEET 1 AA12 LEU A 41 SER A 48 0 SHEET 2 AA12 LEU A 325 ILE A 327 1 O ILE A 326 N ILE A 42 SHEET 3 AA12 ILE A 284 TYR A 287 1 O ALA A 286 N ILE A 327 SHEET 4 AA12 GLY A 259 LYS A 263 1 O ILE A 260 N CYS A 285 SHEET 5 AA12 PHE A 203 LYS A 210 1 O SER A 206 N ILE A 261 SHEET 6 AA12 CYS A 175 PRO A 178 1 O VAL A 176 N LEU A 205 SHEET 7 AA12 TYR A 127 VAL A 132 1 O ILE A 128 N CYS A 175 SHEET 8 AA12 SER A 85 VAL A 91 1 O VAL A 86 N ILE A 129 SHEET 9 AA12 LEU A 41 SER A 48 1 O PHE A 43 N ILE A 87 SHEET 10 AA12 LEU A 325 ILE A 327 1 O ILE A 326 N ILE A 42 SHEET 11 AA12 ILE A 284 TYR A 287 1 O ALA A 286 N ILE A 327 SHEET 12 AA12 LEU A 41 SER A 48 0 LINK NZ ALYS A 263 CG ASHO A 363 1555 1555 1.30 LINK NZ BLYS A 263 CG BSHO A 363 1555 1555 1.30 LINK SG CYS A 133 ZN ZN A 400 1555 1555 2.26 LINK SG CYS A 135 ZN ZN A 400 1555 1555 2.31 LINK SG CYS A 143 ZN ZN A 400 1555 1555 2.31 LINK ZN ZN A 400 O HOH A2269 1555 1555 2.00 CISPEP 1 LYS A 263 PRO A 264 0 0.29 SITE 1 AC1 4 CYS A 133 CYS A 135 CYS A 143 HOH A2269 SITE 1 AC2 9 PHE A 89 ASP A 131 SER A 179 TYR A 207 SITE 2 AC2 9 PHE A 219 LYS A 263 TYR A 287 SER A 290 SITE 3 AC2 9 TYR A 329 CRYST1 102.570 102.570 168.380 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 0.009749 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009749 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005939 0.00000