HEADER TRANSFERASE 08-MAR-11 2YBO TITLE THE X-RAY STRUCTURE OF THE SAM-DEPENDENT UROPORPHYRINOGEN III TITLE 2 METHYLTRANSFERASE NIRE FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH TITLE 3 SAH COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-279; COMPND 5 SYNONYM: PROBABLE UROPORPHYRIN-III C-METHYLTRANSFERASE, COMPND 6 UROPORPHYRINOGEN III METHYLTRANFERASE; COMPND 7 EC: 2.1.1.107; COMPND 8 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 SUMT, TRANSFERASE, NIRE, 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 2YBO 1 REMARK REVDAT 2 28-SEP-11 2YBO 1 JRNL REMARK VERSN REVDAT 1 01-JUN-11 2YBO 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) : 26.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 18294 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) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 915 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) : 1236 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE SET COUNT : 65 REMARK 3 BIN FREE R VALUE : 0.3550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1858 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 195 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.63800 REMARK 3 B22 (A**2) : -0.37000 REMARK 3 B33 (A**2) : -0.26800 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): 0.231 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.203 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.155 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.098 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.915 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.853 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1923 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2618 ; 1.333 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 246 ; 5.587 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 80 ;36.248 ;23.250 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 302 ;14.532 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;18.313 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 309 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1447 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 997 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1303 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 197 ; 0.160 ; 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): 99 ; 0.194 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 34 ; 0.226 ; 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): 1232 ; 0.673 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1960 ; 1.210 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 691 ; 1.664 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 658 ; 2.693 ; 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 : 2 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 11 A 135 REMARK 3 ORIGIN FOR THE GROUP (A): 16.2809 30.9404 24.3623 REMARK 3 T TENSOR REMARK 3 T11: 0.0178 T22: 0.0450 REMARK 3 T33: 0.0188 T12: 0.0040 REMARK 3 T13: 0.0021 T23: -0.0170 REMARK 3 L TENSOR REMARK 3 L11: 3.1229 L22: 1.5223 REMARK 3 L33: 1.8652 L12: -0.9568 REMARK 3 L13: -0.5081 L23: 0.7871 REMARK 3 S TENSOR REMARK 3 S11: -0.0585 S12: -0.1065 S13: 0.0129 REMARK 3 S21: 0.1322 S22: -0.0398 S23: 0.0447 REMARK 3 S31: -0.0121 S32: -0.0990 S33: 0.0983 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 136 A 266 REMARK 3 ORIGIN FOR THE GROUP (A): 35.7541 12.0534 30.7636 REMARK 3 T TENSOR REMARK 3 T11: 0.0270 T22: 0.0344 REMARK 3 T33: 0.0290 T12: 0.0060 REMARK 3 T13: -0.0039 T23: 0.0100 REMARK 3 L TENSOR REMARK 3 L11: 0.7219 L22: 2.1078 REMARK 3 L33: 1.9319 L12: 0.2257 REMARK 3 L13: 0.1067 L23: -0.4729 REMARK 3 S TENSOR REMARK 3 S11: 0.0219 S12: -0.0132 S13: 0.0625 REMARK 3 S21: 0.0135 S22: -0.0701 S23: 0.0127 REMARK 3 S31: -0.0030 S32: 0.0092 S33: 0.0482 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2YBO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1290047560. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19360 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 46.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.1900 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 : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.580 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 1S4D 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): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 24% PEG REMARK 280 6000, 0.1 M TRIS PH 8.0 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 38.40000 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 38.40000 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 30.45000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.55000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.45000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.55000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.40000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.45000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.55000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.40000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.45000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.55000 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: 5230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.4 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 60.90000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 38.40000 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 ALA A -6 REMARK 465 MET A -5 REMARK 465 ALA A -4 REMARK 465 ASP A -3 REMARK 465 ILE 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 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 55 CG CD NE CZ NH1 NH2 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 2082 O HOH A 2082 3555 2.11 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 17.19 58.66 REMARK 500 ALA A 152 119.86 -163.19 REMARK 500 ASP A 169 64.07 -105.90 REMARK 500 SER A 263 -9.71 81.03 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 A2024 DISTANCE = 9.01 ANGSTROMS REMARK 525 HOH A2073 DISTANCE = 6.62 ANGSTROMS 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YBQ 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 AND UROPORPHYRINOGEN III DBREF 2YBO A 1 279 UNP P95417 P95417_PSEAE 1 279 SEQADV 2YBO ALA A -6 UNP P95417 EXPRESSION TAG SEQADV 2YBO MET A -5 UNP P95417 EXPRESSION TAG SEQADV 2YBO ALA A -4 UNP P95417 EXPRESSION TAG SEQADV 2YBO ASP A -3 UNP P95417 EXPRESSION TAG SEQADV 2YBO ILE A -2 UNP P95417 EXPRESSION TAG SEQADV 2YBO GLY A -1 UNP P95417 EXPRESSION TAG SEQADV 2YBO SER A 0 UNP P95417 EXPRESSION TAG SEQADV 2YBO LEU A 280 UNP P95417 EXPRESSION TAG SEQADV 2YBO GLU A 281 UNP P95417 EXPRESSION TAG SEQADV 2YBO HIS A 282 UNP P95417 EXPRESSION TAG SEQADV 2YBO HIS A 283 UNP P95417 EXPRESSION TAG SEQADV 2YBO HIS A 284 UNP P95417 EXPRESSION TAG SEQADV 2YBO HIS A 285 UNP P95417 EXPRESSION TAG SEQADV 2YBO HIS A 286 UNP P95417 EXPRESSION TAG SEQADV 2YBO HIS A 287 UNP P95417 EXPRESSION TAG SEQRES 1 A 294 ALA MET ALA ASP ILE GLY SER MET ASN THR THR VAL ILE SEQRES 2 A 294 PRO PRO SER LEU LEU ASP VAL ASP PHE PRO ALA GLY SER SEQRES 3 A 294 VAL ALA LEU VAL GLY ALA GLY PRO GLY ASP PRO GLY LEU SEQRES 4 A 294 LEU THR LEU ARG ALA TRP ALA LEU LEU GLN GLN ALA GLU SEQRES 5 A 294 VAL VAL VAL TYR ASP ARG LEU VAL ALA ARG GLU LEU ILE SEQRES 6 A 294 ALA LEU LEU PRO GLU SER CYS GLN ARG ILE TYR VAL GLY SEQRES 7 A 294 LYS ARG CYS GLY HIS HIS SER LEU PRO GLN GLU GLU ILE SEQRES 8 A 294 ASN GLU LEU LEU VAL ARG LEU ALA ARG GLN GLN ARG ARG SEQRES 9 A 294 VAL VAL ARG LEU LYS GLY GLY ASP PRO PHE ILE PHE GLY SEQRES 10 A 294 ARG GLY ALA GLU GLU LEU GLU ARG LEU LEU GLU ALA GLY SEQRES 11 A 294 VAL ASP CYS GLN VAL VAL PRO GLY VAL THR ALA ALA SER SEQRES 12 A 294 GLY CYS SER THR TYR ALA GLY ILE PRO LEU THR HIS ARG SEQRES 13 A 294 ASP LEU ALA GLN SER CYS THR PHE VAL THR GLY HIS LEU SEQRES 14 A 294 GLN ASN ASP GLY ARG LEU ASP LEU ASP TRP ALA GLY LEU SEQRES 15 A 294 ALA ARG GLY LYS GLN THR LEU VAL PHE TYR MET GLY LEU SEQRES 16 A 294 GLY ASN LEU ALA GLU ILE ALA ALA ARG LEU VAL GLU HIS SEQRES 17 A 294 GLY LEU ALA SER ASP THR PRO ALA ALA LEU VAL SER GLN SEQRES 18 A 294 GLY THR GLN ALA GLY GLN GLN VAL THR ARG GLY ALA LEU SEQRES 19 A 294 ALA GLU LEU PRO ALA LEU ALA ARG ARG TYR GLN LEU LYS SEQRES 20 A 294 PRO PRO THR LEU ILE VAL VAL GLY GLN VAL VAL ALA LEU SEQRES 21 A 294 PHE ALA GLU ARG ALA MET ALA HIS PRO SER TYR LEU GLY SEQRES 22 A 294 ALA GLY SER PRO VAL SER ARG GLU ALA VAL ALA CYS ALA SEQRES 23 A 294 LEU GLU HIS HIS HIS HIS HIS HIS HET SAH A1267 26 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 HOH *195(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 LEU A 61 1 8 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 GLY A 187 GLY A 189 5 3 HELIX 9 9 ASN A 190 HIS A 201 1 12 HELIX 10 10 GLU A 229 TYR A 237 1 9 HELIX 11 11 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 GLY A 103 1 O VAL A 99 N VAL A 48 SHEET 4 AA 5 VAL A 20 GLY A 26 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 CISPEP 1 PRO A 241 PRO A 242 0 -8.40 SITE 1 AC1 22 PRO A 27 LEU A 52 GLY A 103 GLY A 104 SITE 2 AC1 22 ASP A 105 ILE A 108 PHE A 109 THR A 133 SITE 3 AC1 22 ALA A 134 CYS A 138 TYR A 185 MET A 186 SITE 4 AC1 22 VAL A 212 GLN A 214 GLY A 215 GLN A 217 SITE 5 AC1 22 PRO A 242 THR A 243 LEU A 244 HOH A2022 SITE 6 AC1 22 HOH A2065 HOH A2195 CRYST1 60.900 115.100 76.800 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 0.016420 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008688 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013021 0.00000