HEADER TRANSFERASE 09-MAR-11 2YBQ TITLE THE X-RAY STRUCTURE OF THE SAM-DEPENDENT UROPORPHYRINOGEN III TITLE 2 METHYLTRANSFERASE NIRE FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH TITLE 3 SAH AND UROPORPHYRINOGEN III COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UROPORPHYRINOGEN III METHYLTRANFERASE; COMPND 5 EC: 2.1.1.107; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 STRAIN: PAO1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET32A; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32A_PRES2-4_NIRE KEYWDS TRANSFERASE, HEME D1 BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR S.STORBECK,S.SAHA,J.KRAUSZE,B.U.KLINK,D.W.HEINZ,G.LAYER REVDAT 3 20-DEC-23 2YBQ 1 REMARK REVDAT 2 28-SEP-11 2YBQ 1 JRNL REMARK VERSN REVDAT 1 01-JUN-11 2YBQ 0 JRNL AUTH S.STORBECK,S.SAHA,J.KRAUSZE,B.U.KLINK,D.W.HEINZ,G.LAYER JRNL TITL CRYSTAL STRUCTURE OF THE HEME D1 BIOSYNTHESIS ENZYME NIRE IN JRNL TITL 2 COMPLEX WITH ITS SUBSTRATE REVEALS NEW INSIGHTS INTO THE JRNL TITL 3 CATALYTIC MECHANISM OF S-ADENOSYL-L-METHIONINE-DEPENDENT JRNL TITL 4 UROPORPHYRINOGEN III METHYLTRANSFERASES. JRNL REF J.BIOL.CHEM. V. 286 26754 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21632530 JRNL DOI 10.1074/JBC.M111.239855 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 17443 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 919 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1341 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1817 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : 1.17000 REMARK 3 B33 (A**2) : -1.03000 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): 0.216 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.139 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.846 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.919 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1947 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2652 ; 1.314 ; 2.027 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 239 ; 5.240 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;36.981 ;22.821 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 298 ;14.191 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;20.273 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 301 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1480 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 868 ; 0.201 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1277 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 124 ; 0.129 ; 0.200 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): 68 ; 0.179 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.164 ; 0.200 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): 1201 ; 0.563 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1911 ; 1.025 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 746 ; 1.606 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 741 ; 2.721 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 5 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 13 A 49 REMARK 3 ORIGIN FOR THE GROUP (A): 10.1552 35.5996 16.2873 REMARK 3 T TENSOR REMARK 3 T11: 0.1287 T22: 0.1734 REMARK 3 T33: 0.2455 T12: -0.0332 REMARK 3 T13: 0.0179 T23: 0.0806 REMARK 3 L TENSOR REMARK 3 L11: 6.1912 L22: 0.6541 REMARK 3 L33: 1.2534 L12: 1.5486 REMARK 3 L13: 0.4257 L23: 0.3343 REMARK 3 S TENSOR REMARK 3 S11: 0.0265 S12: 0.0132 S13: 0.5447 REMARK 3 S21: -0.0211 S22: -0.1644 S23: 0.0844 REMARK 3 S31: -0.2371 S32: 0.1349 S33: 0.1379 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 50 A 82 REMARK 3 ORIGIN FOR THE GROUP (A): 12.0945 33.2361 5.7150 REMARK 3 T TENSOR REMARK 3 T11: 0.2755 T22: 0.4264 REMARK 3 T33: 0.2199 T12: -0.0579 REMARK 3 T13: -0.0386 T23: 0.0885 REMARK 3 L TENSOR REMARK 3 L11: 8.1338 L22: 5.0714 REMARK 3 L33: 5.3744 L12: 0.1930 REMARK 3 L13: 0.8983 L23: -1.6550 REMARK 3 S TENSOR REMARK 3 S11: 0.0863 S12: 0.8662 S13: -0.0612 REMARK 3 S21: -0.7644 S22: 0.0200 S23: 0.5051 REMARK 3 S31: -0.2344 S32: -0.3788 S33: -0.1063 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 83 A 171 REMARK 3 ORIGIN FOR THE GROUP (A): 10.2565 20.9624 14.7548 REMARK 3 T TENSOR REMARK 3 T11: 0.0455 T22: 0.1286 REMARK 3 T33: 0.0661 T12: 0.0264 REMARK 3 T13: 0.0267 T23: 0.0210 REMARK 3 L TENSOR REMARK 3 L11: 1.2430 L22: 1.8722 REMARK 3 L33: 1.1868 L12: 1.1327 REMARK 3 L13: 0.6488 L23: 0.0819 REMARK 3 S TENSOR REMARK 3 S11: 0.0536 S12: 0.1815 S13: -0.1446 REMARK 3 S21: -0.0359 S22: -0.0766 S23: -0.2803 REMARK 3 S31: 0.1437 S32: 0.2642 S33: 0.0230 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 172 A 255 REMARK 3 ORIGIN FOR THE GROUP (A): -5.8008 10.5444 5.2337 REMARK 3 T TENSOR REMARK 3 T11: 0.1487 T22: 0.0801 REMARK 3 T33: 0.0461 T12: 0.0013 REMARK 3 T13: -0.0194 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 0.5490 L22: 1.0211 REMARK 3 L33: 1.4178 L12: -0.4401 REMARK 3 L13: 0.2313 L23: 0.6655 REMARK 3 S TENSOR REMARK 3 S11: 0.0228 S12: 0.0176 S13: -0.0026 REMARK 3 S21: -0.1035 S22: -0.0519 S23: 0.0515 REMARK 3 S31: 0.0682 S32: -0.0906 S33: 0.0292 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 256 A 265 REMARK 3 ORIGIN FOR THE GROUP (A): -17.3340 26.7032 9.0634 REMARK 3 T TENSOR REMARK 3 T11: 0.5909 T22: 0.5354 REMARK 3 T33: 0.4499 T12: 0.1485 REMARK 3 T13: -0.0835 T23: 0.0807 REMARK 3 L TENSOR REMARK 3 L11: 6.3324 L22: 13.0666 REMARK 3 L33: 25.8937 L12: -4.1138 REMARK 3 L13: -0.8512 L23: 16.9153 REMARK 3 S TENSOR REMARK 3 S11: 0.2294 S12: 1.2901 S13: 0.0014 REMARK 3 S21: -1.1066 S22: -0.2630 S23: 0.0739 REMARK 3 S31: -1.3547 S32: 0.9100 S33: 0.0336 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2YBQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1290047583. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : SI(100) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18362 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2YBO REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 1.26 M REMARK 280 AMMONIUM SULFATE, 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH 8.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 38.49400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.49400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 31.92650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 58.35100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.92650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 58.35100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.49400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.92650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 58.35100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.49400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.92650 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 58.35100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.4 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 38.49400 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 GLY A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 THR A 3 REMARK 465 THR A 4 REMARK 465 VAL A 5 REMARK 465 ILE A 6 REMARK 465 PRO A 7 REMARK 465 PRO A 8 REMARK 465 SER A 9 REMARK 465 LEU A 10 REMARK 465 LEU A 11 REMARK 465 ASP A 12 REMARK 465 LYS A 72 REMARK 465 ARG A 73 REMARK 465 CYS A 74 REMARK 465 GLY A 75 REMARK 465 HIS A 76 REMARK 465 HIS A 77 REMARK 465 SER A 78 REMARK 465 LEU A 79 REMARK 465 ASN A 164 REMARK 465 ASP A 165 REMARK 465 GLY A 166 REMARK 465 ARG A 167 REMARK 465 ALA A 267 REMARK 465 GLY A 268 REMARK 465 SER A 269 REMARK 465 PRO A 270 REMARK 465 VAL A 271 REMARK 465 SER A 272 REMARK 465 ARG A 273 REMARK 465 GLU A 274 REMARK 465 ALA A 275 REMARK 465 VAL A 276 REMARK 465 ALA A 277 REMARK 465 CYS A 278 REMARK 465 ALA A 279 REMARK 465 LEU A 280 REMARK 465 GLU A 281 REMARK 465 HIS A 282 REMARK 465 HIS A 283 REMARK 465 HIS A 284 REMARK 465 HIS A 285 REMARK 465 HIS A 286 REMARK 465 HIS A 287 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 257 NE - CZ - NH1 ANGL. DEV. = -3.6 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 ARG A 111 17.53 53.32 REMARK 500 ASP A 169 56.55 -100.84 REMARK 500 THR A 216 -6.26 76.26 REMARK 500 SER A 263 -14.23 80.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 1267 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UP2 A 1268 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YBO RELATED DB: PDB REMARK 900 THE X-RAY STRUCTURE OF THE SAM-DEPENDENT UROPORPHYRINOGEN III REMARK 900 METHYLTRANSFERASE NIRE FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH REMARK 900 SAH DBREF 2YBQ A 1 279 UNP P95417 P95417_PSEAE 1 279 SEQADV 2YBQ GLY A -4 UNP P95417 EXPRESSION TAG SEQADV 2YBQ PRO A -3 UNP P95417 EXPRESSION TAG SEQADV 2YBQ LEU A -2 UNP P95417 EXPRESSION TAG SEQADV 2YBQ GLY A -1 UNP P95417 EXPRESSION TAG SEQADV 2YBQ SER A 0 UNP P95417 EXPRESSION TAG SEQADV 2YBQ LEU A 280 UNP P95417 EXPRESSION TAG SEQADV 2YBQ GLU A 281 UNP P95417 EXPRESSION TAG SEQADV 2YBQ HIS A 282 UNP P95417 EXPRESSION TAG SEQADV 2YBQ HIS A 283 UNP P95417 EXPRESSION TAG SEQADV 2YBQ HIS A 284 UNP P95417 EXPRESSION TAG SEQADV 2YBQ HIS A 285 UNP P95417 EXPRESSION TAG SEQADV 2YBQ HIS A 286 UNP P95417 EXPRESSION TAG SEQADV 2YBQ HIS A 287 UNP P95417 EXPRESSION TAG SEQRES 1 A 292 GLY PRO LEU GLY SER MET ASN THR THR VAL ILE PRO PRO SEQRES 2 A 292 SER LEU LEU ASP VAL ASP PHE PRO ALA GLY SER VAL ALA SEQRES 3 A 292 LEU VAL GLY ALA GLY PRO GLY ASP PRO GLY LEU LEU THR SEQRES 4 A 292 LEU ARG ALA TRP ALA LEU LEU GLN GLN ALA GLU VAL VAL SEQRES 5 A 292 VAL TYR ASP ARG LEU VAL ALA ARG GLU LEU ILE ALA LEU SEQRES 6 A 292 LEU PRO GLU SER CYS GLN ARG ILE TYR VAL GLY LYS ARG SEQRES 7 A 292 CYS GLY HIS HIS SER LEU PRO GLN GLU GLU ILE ASN GLU SEQRES 8 A 292 LEU LEU VAL ARG LEU ALA ARG GLN GLN ARG ARG VAL VAL SEQRES 9 A 292 ARG LEU LYS GLY GLY ASP PRO PHE ILE PHE GLY ARG GLY SEQRES 10 A 292 ALA GLU GLU LEU GLU ARG LEU LEU GLU ALA GLY VAL ASP SEQRES 11 A 292 CYS GLN VAL VAL PRO GLY VAL THR ALA ALA SER GLY CYS SEQRES 12 A 292 SER THR TYR ALA GLY ILE PRO LEU THR HIS ARG ASP LEU SEQRES 13 A 292 ALA GLN SER CYS THR PHE VAL THR GLY HIS LEU GLN ASN SEQRES 14 A 292 ASP GLY ARG LEU ASP LEU ASP TRP ALA GLY LEU ALA ARG SEQRES 15 A 292 GLY LYS GLN THR LEU VAL PHE TYR MET GLY LEU GLY ASN SEQRES 16 A 292 LEU ALA GLU ILE ALA ALA ARG LEU VAL GLU HIS GLY LEU SEQRES 17 A 292 ALA SER ASP THR PRO ALA ALA LEU VAL SER GLN GLY THR SEQRES 18 A 292 GLN ALA GLY GLN GLN VAL THR ARG GLY ALA LEU ALA GLU SEQRES 19 A 292 LEU PRO ALA LEU ALA ARG ARG TYR GLN LEU LYS PRO PRO SEQRES 20 A 292 THR LEU ILE VAL VAL GLY GLN VAL VAL ALA LEU PHE ALA SEQRES 21 A 292 GLU ARG ALA MET ALA HIS PRO SER TYR LEU GLY ALA GLY SEQRES 22 A 292 SER PRO VAL SER ARG GLU ALA VAL ALA CYS ALA LEU GLU SEQRES 23 A 292 HIS HIS HIS HIS HIS HIS HET SAH A1267 26 HET UP2 A1268 60 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM UP2 UROPORPHYRINOGEN III FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 UP2 C40 H44 N4 O16 FORMUL 4 HOH *129(H2 O) HELIX 1 1 ASP A 29 LEU A 33 5 5 HELIX 2 2 THR A 34 GLN A 42 1 9 HELIX 3 3 ALA A 54 ALA A 59 1 6 HELIX 4 4 PRO A 80 GLN A 94 1 15 HELIX 5 5 ARG A 111 ALA A 122 1 12 HELIX 6 6 THR A 133 ALA A 142 1 10 HELIX 7 7 ASP A 171 ALA A 176 1 6 HELIX 8 8 ASN A 190 HIS A 201 1 12 HELIX 9 9 GLU A 229 TYR A 237 1 9 HELIX 10 10 GLN A 249 PHE A 254 1 6 SHEET 1 AA 5 GLN A 66 TYR A 69 0 SHEET 2 AA 5 VAL A 46 TYR A 49 1 O VAL A 47 N ILE A 68 SHEET 3 AA 5 VAL A 98 LYS A 102 1 O VAL A 99 N VAL A 48 SHEET 4 AA 5 VAL A 20 GLY A 24 1 O ALA A 21 N ARG A 100 SHEET 5 AA 5 CYS A 126 VAL A 129 1 O GLN A 127 N LEU A 22 SHEET 1 AB 5 CYS A 155 THR A 159 0 SHEET 2 AB 5 THR A 181 TYR A 185 1 O THR A 181 N THR A 156 SHEET 3 AB 5 THR A 243 VAL A 247 -1 O ILE A 245 N PHE A 184 SHEET 4 AB 5 PRO A 208 SER A 213 -1 O ALA A 210 N VAL A 246 SHEET 5 AB 5 GLN A 221 ALA A 226 -1 O GLN A 221 N SER A 213 SHEET 1 AC 2 ALA A 258 HIS A 261 0 SHEET 2 AC 2 TYR A 264 GLY A 266 -1 O TYR A 264 N HIS A 261 CISPEP 1 PRO A 241 PRO A 242 0 -0.85 SITE 1 AC1 23 PRO A 27 LEU A 52 GLY A 103 GLY A 104 SITE 2 AC1 23 ASP A 105 ILE A 108 PHE A 109 THR A 133 SITE 3 AC1 23 ALA A 134 CYS A 138 TYR A 185 MET A 186 SITE 4 AC1 23 VAL A 212 GLN A 214 GLY A 215 GLN A 217 SITE 5 AC1 23 PRO A 242 THR A 243 LEU A 244 UP2 A1268 SITE 6 AC1 23 HOH A2018 HOH A2039 HOH A2123 SITE 1 AC2 21 ASP A 50 ARG A 51 LEU A 52 PHE A 109 SITE 2 AC2 21 ARG A 111 ARG A 149 HIS A 161 LEU A 162 SITE 3 AC2 21 GLN A 163 MET A 186 LEU A 188 GLY A 189 SITE 4 AC2 21 PRO A 241 SAH A1267 HOH A2042 HOH A2123 SITE 5 AC2 21 HOH A2124 HOH A2125 HOH A2126 HOH A2128 SITE 6 AC2 21 HOH A2129 CRYST1 63.853 116.702 76.988 90.00 90.00 90.00 C 2 2 21 8 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 0.015661 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008569 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012989 0.00000