HEADER LYASE 22-FEB-16 5IC2 OBSLTE 07-DEC-16 5IC2 5MHB TITLE PRODUCT-COMPLEX OF E.COLI 5-AMINO LAEVULINIC ACID DEHYDRATASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DELTA-AMINOLEVULINIC ACID DEHYDRATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALADH,PORPHOBILINOGEN SYNTHASE; COMPND 5 EC: 4.2.1.24; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: HEMB, NCF, B0369, JW0361; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TB1; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PUC19 KEYWDS DEHYDRATASE, LYASE, TETRAPYRROLE BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR E.NORTON,P.T.ERSKINE,P.M.SHOOLINGIN-JORDAN,J.B.COOPER REVDAT 4 08-NOV-23 5IC2 1 OBSLTE REVDAT 3 23-JUN-21 5IC2 1 OBSLTE REMARK LINK ATOM REVDAT 2 07-DEC-16 5IC2 1 REVDAT 1 02-MAR-16 5IC2 0 JRNL AUTH N.MILLS-DAVIES,D.BUTLER,E.NORTON,D.THOMPSON,R.GILL,N.AZIM, JRNL AUTH 2 A.COKER,S.P.WOOD,P.T.ERSKINE,J.B.COOPER,M.AKHTAR, JRNL AUTH 3 P.M.SHOOLINGIN-JORDAN JRNL TITL STRUCTURAL STUDIES OF SUBSTRATE- AND PRODUCT-COMPLEXES OF JRNL TITL 2 AMINOLAEVULINIC ACID DEHYDRATASE FROM HUMANS, E.COLI AND THE JRNL TITL 3 HYPERTHERMOPHILE PYROBACULUM CALIDIFONTIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 32551 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 + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1738 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1945 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.1680 REMARK 3 BIN FREE R VALUE SET COUNT : 99 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2484 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 311 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.98000 REMARK 3 B22 (A**2) : 0.98000 REMARK 3 B33 (A**2) : -1.96000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.131 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.137 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.093 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.001 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2573 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2489 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3463 ; 2.256 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5726 ; 1.267 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 326 ; 6.555 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;34.230 ;23.391 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 455 ;14.503 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;21.328 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 385 ; 0.132 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2906 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 569 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1298 ; 1.080 ; 1.440 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1297 ; 1.076 ; 1.439 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1623 ; 1.710 ; 2.152 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1624 ; 1.709 ; 2.154 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1275 ; 1.708 ; 1.690 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1275 ; 1.633 ; 1.690 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1840 ; 2.680 ; 2.445 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3080 ; 8.118 ;13.714 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2949 ; 7.846 ;12.428 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 406 REMARK 3 ORIGIN FOR THE GROUP (A): -15.4187 -25.4681 14.2852 REMARK 3 T TENSOR REMARK 3 T11: 0.1987 T22: 0.1052 REMARK 3 T33: 0.1245 T12: -0.1094 REMARK 3 T13: 0.0678 T23: 0.0174 REMARK 3 L TENSOR REMARK 3 L11: 0.8183 L22: 0.4794 REMARK 3 L33: 1.7487 L12: -0.0505 REMARK 3 L13: -0.0044 L23: -0.0132 REMARK 3 S TENSOR REMARK 3 S11: -0.0224 S12: -0.1697 S13: -0.1835 REMARK 3 S21: 0.0815 S22: -0.0139 S23: 0.1073 REMARK 3 S31: 0.4538 S32: -0.2701 S33: 0.0363 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5IC2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 5 REMARK 5 OBSOLETION UPON AUTHORS REQUEST, NO KNOWN SUPERSEDING ENTRY REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000216524. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 - 8.4 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 : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8342 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 : 34487 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 23.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.36800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 1B4E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CONCENTRATION 7 MG/ML MIXED REMARK 280 WITH AN EQUAL VOLUME OF WELL SOLUTION MADE OF 200 MM TRIS PH 8.0 REMARK 280 - 8.4, 2% AS, 200 MICROMOLAR ZINC SULPHATE, 6 MM BME AND 3 MM REMARK 280 PBG, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 64.08550 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 64.08550 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 71.37950 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 64.08550 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 64.08550 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 71.37950 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 64.08550 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 64.08550 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 71.37950 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 64.08550 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 64.08550 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 71.37950 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 64.08550 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 64.08550 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 71.37950 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 64.08550 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 64.08550 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 71.37950 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 64.08550 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 64.08550 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 71.37950 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 64.08550 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 64.08550 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 71.37950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 55070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 74570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -746.0 KCAL/MOL 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 8 -1.000000 0.000000 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 A 756 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 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 12 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 101 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ASP A 160 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 176 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 289 CB - CG - OD1 ANGL. DEV. = 8.1 DEGREES REMARK 500 LYS A 302 CG - CD - CE ANGL. DEV. = -18.9 DEGREES REMARK 500 LYS A 302 CD - CE - NZ ANGL. DEV. = 22.0 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 HIS A 84 55.04 -145.44 REMARK 500 CYS A 130 39.23 -75.23 REMARK 500 TYR A 219 -57.05 -131.84 REMARK 500 PRO A 248 172.98 -52.22 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 A 811 DISTANCE = 6.55 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 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 40 OE2 REMARK 620 2 GLU A 40 OE2 0.0 REMARK 620 3 HIS A 84 NE2 115.6 115.6 REMARK 620 4 HIS A 84 NE2 115.6 115.6 0.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 120 SG REMARK 620 2 CYS A 122 SG 117.0 REMARK 620 3 CYS A 130 SG 108.2 111.4 REMARK 620 4 PBG A 401 N1 101.1 96.2 122.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 232 OE1 REMARK 620 2 HOH A 515 O 172.8 REMARK 620 3 HOH A 516 O 89.1 93.6 REMARK 620 4 HOH A 576 O 87.9 89.3 177.0 REMARK 620 5 HOH A 582 O 84.2 89.4 85.0 94.5 REMARK 620 6 HOH A 726 O 99.4 87.2 91.8 88.9 175.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PBG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 407 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1B4E RELATED DB: PDB REMARK 900 1B4E IS SAME PROTEIN COMPLEXED WITH LEVULINIC ACID DBREF 5IC2 A 1 324 UNP P0ACB2 HEM2_ECOLI 1 324 SEQRES 1 A 324 MET THR ASP LEU ILE GLN ARG PRO ARG ARG LEU ARG LYS SEQRES 2 A 324 SER PRO ALA LEU ARG ALA MET PHE GLU GLU THR THR LEU SEQRES 3 A 324 SER LEU ASN ASP LEU VAL LEU PRO ILE PHE VAL GLU GLU SEQRES 4 A 324 GLU ILE ASP ASP TYR LYS ALA VAL GLU ALA MET PRO GLY SEQRES 5 A 324 VAL MET ARG ILE PRO GLU LYS HIS LEU ALA ARG GLU ILE SEQRES 6 A 324 GLU ARG ILE ALA ASN ALA GLY ILE ARG SER VAL MET THR SEQRES 7 A 324 PHE GLY ILE SER HIS HIS THR ASP GLU THR GLY SER ASP SEQRES 8 A 324 ALA TRP ARG GLU ASP GLY LEU VAL ALA ARG MET SER ARG SEQRES 9 A 324 ILE CYS LYS GLN THR VAL PRO GLU MET ILE VAL MET SER SEQRES 10 A 324 ASP THR CYS PHE CYS GLU TYR THR SER HIS GLY HIS CYS SEQRES 11 A 324 GLY VAL LEU CYS GLU HIS GLY VAL ASP ASN ASP ALA THR SEQRES 12 A 324 LEU GLU ASN LEU GLY LYS GLN ALA VAL VAL ALA ALA ALA SEQRES 13 A 324 ALA GLY ALA ASP PHE ILE ALA PRO SER ALA ALA MET ASP SEQRES 14 A 324 GLY GLN VAL GLN ALA ILE ARG GLN ALA LEU ASP ALA ALA SEQRES 15 A 324 GLY PHE LYS ASP THR ALA ILE MET SER TYR SER THR LYS SEQRES 16 A 324 PHE ALA SER SER PHE TYR GLY PRO PHE ARG GLU ALA ALA SEQRES 17 A 324 GLY SER ALA LEU LYS GLY ASP ARG LYS SER TYR GLN MET SEQRES 18 A 324 ASN PRO MET ASN ARG ARG GLU ALA ILE ARG GLU SER LEU SEQRES 19 A 324 LEU ASP GLU ALA GLN GLY ALA ASP CYS LEU MET VAL LYS SEQRES 20 A 324 PRO ALA GLY ALA TYR LEU ASP ILE VAL ARG GLU LEU ARG SEQRES 21 A 324 GLU ARG THR GLU LEU PRO ILE GLY ALA TYR GLN VAL SER SEQRES 22 A 324 GLY GLU TYR ALA MET ILE LYS PHE ALA ALA LEU ALA GLY SEQRES 23 A 324 ALA ILE ASP GLU GLU LYS VAL VAL LEU GLU SER LEU GLY SEQRES 24 A 324 SER ILE LYS ARG ALA GLY ALA ASP LEU ILE PHE SER TYR SEQRES 25 A 324 PHE ALA LEU ASP LEU ALA GLU LYS LYS ILE LEU ARG HET PBG A 401 16 HET ZN A 402 1 HET ZN A 403 1 HET ZN A 404 1 HET GOL A 405 6 HET GOL A 406 6 HET GOL A 407 6 HETNAM PBG 3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROL-3- HETNAM 2 PBG YL]PROPANOIC ACID HETNAM ZN ZINC ION HETNAM GOL GLYCEROL 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 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 PBG C10 H14 N2 O4 FORMUL 3 ZN 3(ZN 2+) FORMUL 6 GOL 3(C3 H8 O3) FORMUL 9 HOH *311(H2 O) HELIX 1 AA1 ARG A 7 LYS A 13 5 7 HELIX 2 AA2 SER A 14 GLU A 22 1 9 HELIX 3 AA3 SER A 27 ASN A 29 5 3 HELIX 4 AA4 HIS A 60 ALA A 71 1 12 HELIX 5 AA5 GLY A 89 ARG A 94 5 6 HELIX 6 AA6 GLY A 97 VAL A 110 1 14 HELIX 7 AA7 ASP A 139 GLY A 158 1 20 HELIX 8 AA8 GLY A 170 ALA A 182 1 13 HELIX 9 AA9 SER A 198 PHE A 200 5 3 HELIX 10 AB1 TYR A 201 GLY A 209 1 9 HELIX 11 AB2 ASN A 225 GLN A 239 1 15 HELIX 12 AB3 TYR A 252 GLU A 261 1 10 HELIX 13 AB4 VAL A 272 ALA A 285 1 14 HELIX 14 AB5 ASP A 289 ALA A 304 1 16 HELIX 15 AB6 PHE A 313 LYS A 320 1 8 SHEET 1 AA1 7 LYS A 45 ALA A 46 0 SHEET 2 AA1 7 MET A 54 PRO A 57 -1 O ARG A 55 N LYS A 45 SHEET 3 AA1 7 LEU A 31 GLU A 38 1 N PHE A 36 O ILE A 56 SHEET 4 AA1 7 SER A 75 ILE A 81 1 O PHE A 79 N VAL A 37 SHEET 5 AA1 7 ILE A 114 THR A 119 1 O MET A 116 N VAL A 76 SHEET 6 AA1 7 PHE A 161 PRO A 164 1 O PHE A 161 N SER A 117 SHEET 7 AA1 7 ALA A 188 ILE A 189 1 O ALA A 188 N ILE A 162 SHEET 1 AA2 7 LYS A 45 ALA A 46 0 SHEET 2 AA2 7 MET A 54 PRO A 57 -1 O ARG A 55 N LYS A 45 SHEET 3 AA2 7 LEU A 31 GLU A 38 1 N PHE A 36 O ILE A 56 SHEET 4 AA2 7 LEU A 308 PHE A 310 1 O ILE A 309 N VAL A 32 SHEET 5 AA2 7 ILE A 267 TYR A 270 1 N ALA A 269 O PHE A 310 SHEET 6 AA2 7 LEU A 244 LYS A 247 1 N LEU A 244 O GLY A 268 SHEET 7 AA2 7 THR A 194 LYS A 195 1 N THR A 194 O MET A 245 SHEET 1 AA3 2 LEU A 133 CYS A 134 0 SHEET 2 AA3 2 GLY A 137 VAL A 138 -1 O GLY A 137 N CYS A 134 LINK OE2 GLU A 40 ZN ZN A 402 1555 1555 2.00 LINK OE2 GLU A 40 ZN ZN A 402 1555 16445 1.90 LINK NE2 HIS A 84 ZN ZN A 402 1555 1555 2.42 LINK NE2 HIS A 84 ZN ZN A 402 1555 16445 2.15 LINK SG CYS A 120 ZN ZN A 403 1555 1555 2.19 LINK SG CYS A 122 ZN ZN A 403 1555 1555 2.31 LINK SG CYS A 130 ZN ZN A 403 1555 1555 2.30 LINK OE1 GLU A 232 ZN ZN A 404 1555 1555 2.14 LINK N1 PBG A 401 ZN ZN A 403 1555 1555 2.33 LINK ZN ZN A 404 O HOH A 515 1555 1555 2.31 LINK ZN ZN A 404 O HOH A 516 1555 1555 2.22 LINK ZN ZN A 404 O HOH A 576 1555 1555 2.14 LINK ZN ZN A 404 O HOH A 582 1555 1555 2.24 LINK ZN ZN A 404 O HOH A 726 1555 1555 2.38 CISPEP 1 LYS A 247 PRO A 248 0 -16.75 SITE 1 AC1 16 CYS A 120 CYS A 122 SER A 165 LYS A 195 SITE 2 AC1 16 TYR A 201 PHE A 204 ARG A 205 ARG A 216 SITE 3 AC1 16 GLN A 220 LYS A 247 TYR A 270 VAL A 272 SITE 4 AC1 16 SER A 273 TYR A 312 ZN A 403 HOH A 579 SITE 1 AC2 2 GLU A 40 HIS A 84 SITE 1 AC3 4 CYS A 120 CYS A 122 CYS A 130 PBG A 401 SITE 1 AC4 6 GLU A 232 HOH A 515 HOH A 516 HOH A 576 SITE 2 AC4 6 HOH A 582 HOH A 726 SITE 1 AC5 3 LEU A 295 GLU A 296 HOH A 609 SITE 1 AC6 7 GLU A 290 GLU A 291 PHE A 313 ASP A 316 SITE 2 AC6 7 LYS A 320 ILE A 322 HOH A 631 SITE 1 AC7 6 ALA A 197 ASP A 215 ARG A 216 LYS A 217 SITE 2 AC7 6 HOH A 541 HOH A 665 CRYST1 128.171 128.171 142.759 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 0.007802 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007802 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007005 0.00000