HEADER LYASE 23-NOV-16 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; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: HEMB, NCF, B0369, JW0361; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DEHYDRATASE, LYASE, TETRAPYRROLE BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR E.NORTON,P.T.ERSKINE,P.M.SHOOLINGIN-JORDAN,J.B.COOPER REVDAT 5 17-JAN-24 5MHB 1 LINK REVDAT 4 17-JUL-19 5MHB 1 REMARK REVDAT 3 25-JAN-17 5MHB 1 JRNL REVDAT 2 11-JAN-17 5MHB 1 JRNL REVDAT 1 07-DEC-16 5MHB 0 SPRSDE 07-DEC-16 5MHB 5IC2 JRNL AUTH N.MILLS-DAVIES,D.BUTLER,E.NORTON,D.THOMPSON,M.SARWAR,J.GUO, JRNL AUTH 2 R.GILL,N.AZIM,A.COKER,S.P.WOOD,P.T.ERSKINE,L.COATES, JRNL AUTH 3 J.B.COOPER,N.RASHID,M.AKHTAR,P.M.SHOOLINGIN-JORDAN JRNL TITL STRUCTURAL STUDIES OF SUBSTRATE AND PRODUCT COMPLEXES OF JRNL TITL 2 5-AMINOLAEVULINIC ACID DEHYDRATASE FROM HUMANS, ESCHERICHIA JRNL TITL 3 COLI AND THE HYPERTHERMOPHILE PYROBACULUM CALIDIFONTIS. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 73 9 2017 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 28045381 JRNL DOI 10.1107/S2059798316019525 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) : 95.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 32987 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1761 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) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2225 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 111 REMARK 3 BIN FREE R VALUE : 0.3030 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 : 327 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.62000 REMARK 3 B22 (A**2) : 0.62000 REMARK 3 B33 (A**2) : -1.24000 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): 0.123 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.135 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.475 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2573 ; 0.028 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2489 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3463 ; 2.541 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5726 ; 1.346 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 326 ; 6.664 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;34.421 ;23.391 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 455 ;14.638 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;19.411 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 385 ; 0.162 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2906 ; 0.014 ; 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 ; 1.933 ; 2.114 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1297 ; 1.933 ; 2.113 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1623 ; 2.894 ; 3.158 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1624 ; 2.893 ; 3.159 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1275 ; 3.005 ; 2.506 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1275 ; 2.922 ; 2.507 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1840 ; 4.700 ; 3.612 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3077 ; 7.634 ;18.716 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2942 ; 7.391 ;17.730 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): -15.4608 -25.5379 14.2922 REMARK 3 T TENSOR REMARK 3 T11: 0.1868 T22: 0.0934 REMARK 3 T33: 0.0310 T12: -0.1029 REMARK 3 T13: 0.0495 T23: -0.0168 REMARK 3 L TENSOR REMARK 3 L11: 0.3228 L22: 0.0184 REMARK 3 L33: 0.9253 L12: -0.0187 REMARK 3 L13: 0.0551 L23: 0.0043 REMARK 3 S TENSOR REMARK 3 S11: -0.0077 S12: -0.0825 S13: 0.0119 REMARK 3 S21: -0.0103 S22: -0.0072 S23: -0.0200 REMARK 3 S31: 0.2318 S32: -0.1411 S33: 0.0148 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 5MHB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1200002450. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-97; 03-JUN-98 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.0 - 8.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ESRF; EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BM14; X11 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.069; 0.834 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE; MAR REMARK 200 SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM 5.8.0107 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34248 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 36.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 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) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.72500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1B4E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ALAD AT 7 MG PER ML MIXED WITH EQUAL REMARK 280 VOLUME OF WELL SOLUTION: 200 MM TRIS PH 8.0 - 8.4, 2 % SATURATED REMARK 280 AMMONIUM SULPHATE, 200 MICROM ZINC SULPHATE, 6 MM BETA- REMARK 280 MERCAPTOETHANOL AND 3 MM PORPHOBILINOGEN. CRYSTALS WERE GROWN IN REMARK 280 THE DARK., PH 8.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 64.30950 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 64.30950 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 71.40750 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 64.30950 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 64.30950 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 71.40750 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 64.30950 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 64.30950 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 71.40750 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 64.30950 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 64.30950 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 71.40750 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 64.30950 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 64.30950 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 71.40750 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 64.30950 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 64.30950 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 71.40750 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 64.30950 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 64.30950 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 71.40750 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 64.30950 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 64.30950 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 71.40750 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 54960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 74300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -743.0 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 800 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: 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 708 O HOH A 721 2.09 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 689 O HOH A 739 5555 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 124 CE1 TYR A 124 CZ 0.105 REMARK 500 SER A 165 CB SER A 165 OG -0.091 REMARK 500 ARG A 227 CZ ARG A 227 NH1 0.095 REMARK 500 CYS A 243 CB CYS A 243 SG 0.120 REMARK 500 GLU A 261 CD GLU A 261 OE1 -0.069 REMARK 500 GLU A 290 CD GLU A 290 OE1 -0.098 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 ASP A 42 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 101 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP A 160 CB - CG - OD1 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A 176 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ASP A 186 CB - CG - OD1 ANGL. DEV. = 8.2 DEGREES REMARK 500 ASP A 186 CB - CG - OD2 ANGL. DEV. = -8.9 DEGREES REMARK 500 ARG A 227 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ASP A 289 CB - CG - OD1 ANGL. DEV. = 9.4 DEGREES REMARK 500 ASP A 289 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 LYS A 302 CD - CE - NZ ANGL. DEV. = 22.1 DEGREES REMARK 500 ASP A 307 CB - CG - OD1 ANGL. DEV. = -6.6 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 GLU A 40 34.11 70.40 REMARK 500 HIS A 84 51.63 -144.25 REMARK 500 CYS A 130 34.24 -71.70 REMARK 500 PHE A 184 56.54 -112.62 REMARK 500 TYR A 219 -51.34 -126.55 REMARK 500 PRO A 248 173.43 -49.44 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 827 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 OE1 REMARK 620 2 GLU A 40 OE2 57.3 REMARK 620 3 GLU A 40 OE2 57.3 0.0 REMARK 620 4 HIS A 84 NE2 111.3 132.2 132.2 REMARK 620 5 HIS A 84 NE2 111.3 132.2 132.2 0.0 REMARK 620 N 1 2 3 4 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 118.0 REMARK 620 3 CYS A 130 SG 105.2 115.5 REMARK 620 4 PBG A 401 N1 104.1 91.4 122.6 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 516 O 88.1 REMARK 620 3 HOH A 535 O 170.9 96.6 REMARK 620 4 HOH A 560 O 86.3 174.3 89.1 REMARK 620 5 HOH A 584 O 86.7 89.6 85.6 90.5 REMARK 620 6 HOH A 740 O 97.6 91.5 90.1 88.8 175.6 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 DBREF 5MHB 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 *327(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 ALA A 163 N THR A 119 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 LYS A 247 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 OE1 GLU A 40 ZN ZN A 402 1555 1555 2.55 LINK OE2 GLU A 40 ZN ZN A 402 1555 1555 1.73 LINK OE2 GLU A 40 ZN ZN A 402 1555 16445 2.12 LINK NE2 HIS A 84 ZN ZN A 402 1555 1555 2.52 LINK NE2 HIS A 84 ZN ZN A 402 1555 16445 2.16 LINK SG CYS A 120 ZN ZN A 403 1555 1555 2.19 LINK SG CYS A 122 ZN ZN A 403 1555 1555 2.38 LINK SG CYS A 130 ZN ZN A 403 1555 1555 2.33 LINK OE1 GLU A 232 ZN ZN A 404 1555 1555 2.20 LINK N1 PBG A 401 ZN ZN A 403 1555 1555 2.32 LINK ZN ZN A 404 O HOH A 516 1555 1555 2.24 LINK ZN ZN A 404 O HOH A 535 1555 1555 2.34 LINK ZN ZN A 404 O HOH A 560 1555 1555 2.15 LINK ZN ZN A 404 O HOH A 584 1555 1555 2.24 LINK ZN ZN A 404 O HOH A 740 1555 1555 2.40 CISPEP 1 LYS A 247 PRO A 248 0 -19.95 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 522 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 516 HOH A 535 HOH A 560 SITE 2 AC4 6 HOH A 584 HOH A 740 SITE 1 AC5 3 LEU A 295 GLU A 296 HOH A 591 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 669 SITE 1 AC7 6 ALA A 197 SER A 199 ASP A 215 ARG A 216 SITE 2 AC7 6 LYS A 217 HOH A 530 CRYST1 128.619 128.619 142.815 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 0.007775 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007775 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007002 0.00000