HEADER LYASE 12-JUL-12 4B28 TITLE CRYSTAL STRUCTURE OF DMSP LYASE RDDDDP FROM ROSEOBACTER DENITRIFICANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLOPEPTIDASE, FAMILY M24, PUTATIVE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DMSP LYASE RDDDDP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ROSEOBACTER DENITRIFICANS OCH 114; SOURCE 3 ORGANISM_TAXID: 375451; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: STAR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28; SOURCE 10 OTHER_DETAILS: GERMAN COLLECTION OF MICROORGANISMS (DSM) KEYWDS LYASE, IMETHYLSULFONIOPROIONATE, ACRYLATE, DIMETHYLSULFIDE EXPDTA X-RAY DIFFRACTION AUTHOR J.H.HEHEMANN,A.LAW,L.REDECKE,A.B.BORASTON REVDAT 2 06-AUG-14 4B28 1 JRNL REVDAT 1 25-JUL-12 4B28 0 JRNL AUTH J.H.HEHEMANN,A.LAW,L.REDECKE,A.B.BORASTON JRNL TITL THE STRUCTURE OF RDDDDP FROM ROSEOBACTER DENITRIFICANS JRNL TITL 2 REVEALS THAT DMSP LYASES IN THE DDDP-FAMILY ARE JRNL TITL 3 METALLOENZYMES. JRNL REF PLOS ONE V. 9 03128 2014 JRNL REFN ISSN 1932-6203 JRNL PMID 25054772 JRNL DOI 10.1371/JOURNAL.PONE.0103128 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 98.45 REMARK 3 NUMBER OF REFLECTIONS : 27928 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) : 0.20851 REMARK 3 R VALUE (WORKING SET) : 0.20619 REMARK 3 FREE R VALUE : 0.25150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1496 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) : 2.150 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.206 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1846 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.286 REMARK 3 BIN FREE R VALUE SET COUNT : 94 REMARK 3 BIN FREE R VALUE : 0.311 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3394 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.853 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.32 REMARK 3 B22 (A**2) : -2.32 REMARK 3 B33 (A**2) : 3.48 REMARK 3 B12 (A**2) : -1.16 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.234 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.198 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.144 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.576 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3474 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4723 ; 1.265 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 438 ; 6.029 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 168 ;29.468 ;23.750 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 547 ;14.551 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;18.607 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 509 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2715 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2175 ; 0.538 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3474 ; 1.012 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1299 ; 1.705 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1248 ; 2.716 ; 4.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 4B28 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JUL-12. REMARK 100 THE PDBE ID CODE IS EBI-53225. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3779 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD 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 : 33321 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.00 REMARK 200 RESOLUTION RANGE LOW (A) : 58.42 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 200 DATA REDUNDANCY : 12.3 REMARK 200 R MERGE (I) : 0.12 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.80 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) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 45.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.9 REMARK 200 R MERGE FOR SHELL (I) : 0.64 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.20 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.6 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4-4.5 M SODIUM CHLORIDE AND 0.1 REMARK 280 M BIS TRIS PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 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 66.71500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 66.71500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 66.71500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 66.71500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 66.71500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 66.71500 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: 8030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -105.7 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -22 REMARK 465 GLY A -21 REMARK 465 SER A -20 REMARK 465 SER A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 SER A -12 REMARK 465 SER A -11 REMARK 465 GLY A -10 REMARK 465 LEU A -9 REMARK 465 VAL A -8 REMARK 465 PRO A -7 REMARK 465 ARG A -6 REMARK 465 GLY A -5 REMARK 465 SER A -4 REMARK 465 HIS A -3 REMARK 465 MET A -2 REMARK 465 ALA A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 ARG A 3 REMARK 465 HIS A 4 REMARK 465 PHE A 5 REMARK 465 ASN A 6 REMARK 465 ALA A 7 REMARK 465 THR A 8 REMARK 465 VAL A 446 REMARK 465 GLU A 447 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 9 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 10 CG CD CE NZ REMARK 470 SER A 14 OG REMARK 470 ARG A 15 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 46 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 57 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 61 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 118 CG CD CE NZ REMARK 470 ARG A 171 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 184 CG CD NE CZ NH1 NH2 REMARK 470 SER A 253 OG REMARK 470 LYS A 318 CG CD CE NZ REMARK 470 GLU A 339 CG CD OE1 OE2 REMARK 470 LYS A 342 CG CD CE NZ REMARK 470 LYS A 363 CG CD CE NZ REMARK 470 ASP A 429 CG OD1 OD2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASN A 99 OD1 ND2 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 OD1 ASP A 195 O HOH A 2098 2.19 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 2176 O HOH A 2176 12555 1.48 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 ASN A 99 CG ASN A 99 ND2 -0.393 REMARK 500 ASN A 99 CG ASN A 99 OD1 0.204 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 ASN A 99 CB - CG - ND2 ANGL. DEV. = 15.3 DEGREES REMARK 500 ASN A 99 CB - CG - OD1 ANGL. DEV. = -29.5 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 SER A 14 44.35 -76.68 REMARK 500 ASN A 25 75.16 -67.16 REMARK 500 ASP A 88 13.88 59.98 REMARK 500 ASN A 91 109.58 -160.78 REMARK 500 SER A 120 47.27 -141.68 REMARK 500 ALA A 167 57.09 -145.65 REMARK 500 PHE A 278 0.17 90.21 REMARK 500 ASP A 297 58.21 33.97 REMARK 500 CYS A 376 -168.70 -174.81 REMARK 500 REMARK 500 REMARK: NULL 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 FE A1446 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 295 OD1 REMARK 620 2 ASP A 295 OD2 56.8 REMARK 620 3 ASP A 297 OD1 74.1 87.0 REMARK 620 4 ASP A 307 OD1 72.9 129.4 74.0 REMARK 620 5 FE A1447 FE 160.7 130.9 120.9 98.4 REMARK 620 6 GLU A 421 OE1 88.2 100.8 152.7 81.0 73.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A1447 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 FE A1446 FE REMARK 620 2 GLU A 406 OE2 122.8 REMARK 620 3 GLU A 421 OE2 91.5 87.3 REMARK 620 4 ASP A 307 OD2 65.6 169.9 86.8 REMARK 620 5 HIS A 371 NE2 147.8 89.4 91.5 82.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A1446 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A1447 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4B28 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DMSP LYASE RDDDDP FROM ROSEOBACTER REMARK 900 DENITRIFICANS REMARK 999 REMARK 999 SEQUENCE REMARK 999 RECOMBINANT PROTEIN CONTAINS N-TERMINAL HEXA-HISTIDINE TAG REMARK 999 WHICH CAN BE REMOVED WITH THROMBIN PROTEASE DBREF 4B28 A 1 447 UNP Q166H0 Q166H0_ROSDO 1 447 SEQADV 4B28 MET A -22 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 GLY A -21 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 SER A -20 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 SER A -19 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 HIS A -18 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 HIS A -17 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 HIS A -16 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 HIS A -15 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 HIS A -14 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 HIS A -13 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 SER A -12 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 SER A -11 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 GLY A -10 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 LEU A -9 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 VAL A -8 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 PRO A -7 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 ARG A -6 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 GLY A -5 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 SER A -4 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 HIS A -3 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 MET A -2 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 ALA A -1 UNP Q166H0 EXPRESSION TAG SEQADV 4B28 SER A 0 UNP Q166H0 EXPRESSION TAG SEQRES 1 A 470 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 470 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET ASN ARG SEQRES 3 A 470 HIS PHE ASN ALA THR ARG LYS ILE ASP PRO SER ARG GLY SEQRES 4 A 470 ALA THR LEU GLY ASP GLY SER PRO ASN ASP MET ASN ARG SEQRES 5 A 470 VAL GLU ILE GLY PRO THR GLN LEU ALA PHE ALA GLU TRP SEQRES 6 A 470 HIS THR ALA ARG LEU ASP LEU PRO ASP LEU ALA ALA MET SEQRES 7 A 470 ARG ARG PHE ARG HIS ARG ARG LEU THR ASP HIS VAL VAL SEQRES 8 A 470 ALA ARG GLY TYR ALA GLY LEU LEU MET PHE ASP PRO LEU SEQRES 9 A 470 ASN ILE ARG TYR ALA THR ASP SER THR ASN MET GLN LEU SEQRES 10 A 470 TRP ASN THR HIS ASN PRO PHE ARG ALA THR LEU LEU CYS SEQRES 11 A 470 ALA ASP GLY TYR MET VAL MET TRP ASP TYR LYS ASN SER SEQRES 12 A 470 PRO PHE LEU SER GLU PHE ASN PRO LEU VAL ARG GLU GLN SEQRES 13 A 470 ARG ALA GLY ALA ASP LEU PHE TYR PHE ASP ARG GLY ASP SEQRES 14 A 470 LYS VAL ASP VAL ALA ALA ASP VAL PHE ALA ASN GLU VAL SEQRES 15 A 470 ARG ILE LEU LEU ARG ASP HIS ALA PRO GLY LEU ARG ARG SEQRES 16 A 470 LEU ALA VAL ASP LYS VAL MET LEU HIS GLY LEU ARG ALA SEQRES 17 A 470 LEU GLN ALA GLN GLY PHE GLU ILE MET ASP GLY GLU GLU SEQRES 18 A 470 VAL THR GLU LYS ALA ARG SER VAL LYS GLY PRO ASP GLU SEQRES 19 A 470 ILE ARG ALA MET ARG CYS ALA SER HIS ALA CYS GLU VAL SEQRES 20 A 470 ALA VAL ARG LYS MET GLU ASP PHE ALA ARG SER LYS VAL SEQRES 21 A 470 GLY ASP GLY VAL THR CYS GLU ASN ASP ILE TRP ALA ILE SEQRES 22 A 470 LEU HIS SER GLU ASN VAL ARG ARG GLY GLY GLU TRP ILE SEQRES 23 A 470 GLU THR ARG LEU LEU ALA SER GLY PRO ARG SER ASN PRO SEQRES 24 A 470 TRP PHE GLN GLU CYS GLY PRO ARG VAL CYS GLN ARG ASN SEQRES 25 A 470 GLU ILE ILE SER PHE ASP THR ASP LEU VAL GLY ALA TYR SEQRES 26 A 470 GLY ILE CYS THR ASP ILE SER ARG SER TRP TRP ILE GLY SEQRES 27 A 470 ASP GLN LYS PRO ARG ALA ASP MET ILE TYR ALA MET GLN SEQRES 28 A 470 HIS GLY VAL GLU HIS ILE ARG THR ASN MET GLU MET LEU SEQRES 29 A 470 LYS PRO GLY VAL MET ILE PRO GLU LEU SER ALA ASN THR SEQRES 30 A 470 HIS VAL LEU ASP ALA LYS PHE GLN LYS GLN LYS TYR GLY SEQRES 31 A 470 CYS LEU MET HIS GLY VAL GLY LEU CYS ASP GLU TRP PRO SEQRES 32 A 470 LEU VAL ALA TYR PRO ASP HIS ALA VAL ALA GLY ALA TYR SEQRES 33 A 470 ASP TYR PRO LEU GLU PRO GLY MET THR LEU CYS VAL GLU SEQRES 34 A 470 ALA LEU ILE SER GLU GLU GLY GLY ASP PHE SER ILE LYS SEQRES 35 A 470 LEU GLU ASP GLN VAL LEU ILE THR GLU ASP GLY TYR GLU SEQRES 36 A 470 ASN LEU THR LYS TYR PRO PHE ASP PRO ALA LEU MET GLY SEQRES 37 A 470 VAL GLU HET FE A1446 1 HET FE A1447 1 HETNAM FE FE (III) ION FORMUL 2 FE 2(FE 3+) FORMUL 3 HOH *201(H2 O) HELIX 1 1 THR A 35 ALA A 45 1 11 HELIX 2 2 ASP A 51 ARG A 70 1 20 HELIX 3 3 ASP A 79 ASP A 88 1 10 HELIX 4 4 MET A 92 ASN A 99 1 8 HELIX 5 5 SER A 120 GLU A 125 5 6 HELIX 6 6 PHE A 140 GLY A 145 1 6 HELIX 7 7 LYS A 147 ALA A 167 1 21 HELIX 8 8 MET A 179 GLN A 189 1 11 HELIX 9 9 GLY A 196 SER A 205 1 10 HELIX 10 10 GLY A 208 VAL A 237 1 30 HELIX 11 11 CYS A 243 ARG A 257 1 15 HELIX 12 12 PRO A 272 ASN A 275 5 4 HELIX 13 13 ALA A 301 GLY A 303 5 3 HELIX 14 14 ARG A 320 MET A 340 1 21 HELIX 15 15 MET A 346 ASN A 353 1 8 HELIX 16 16 ASP A 358 LYS A 363 1 6 HELIX 17 17 ASP A 440 GLY A 445 1 6 SHEET 1 AA 6 GLU A 132 ARG A 134 0 SHEET 2 AA 6 MET A 112 TRP A 115 1 O MET A 114 N ARG A 134 SHEET 3 AA 6 ALA A 103 CYS A 107 -1 O ALA A 103 N TRP A 115 SHEET 4 AA 6 GLY A 74 MET A 77 -1 O LEU A 75 N LEU A 106 SHEET 5 AA 6 ARG A 172 VAL A 175 1 O ALA A 174 N LEU A 76 SHEET 6 AA 6 GLU A 192 ASP A 195 1 O GLU A 192 N LEU A 173 SHEET 1 AB 3 TRP A 262 ILE A 263 0 SHEET 2 AB 3 LEU A 298 VAL A 299 -1 N VAL A 299 O TRP A 262 SHEET 3 AB 3 CYS A 305 THR A 306 -1 O THR A 306 N LEU A 298 SHEET 1 AC 3 LEU A 268 SER A 270 0 SHEET 2 AC 3 GLU A 290 ASP A 295 -1 O SER A 293 N ALA A 269 SHEET 3 AC 3 SER A 309 ILE A 314 -1 O ARG A 310 N PHE A 294 SHEET 1 AD 5 ASP A 377 VAL A 382 0 SHEET 2 AD 5 MET A 370 VAL A 373 -1 O MET A 370 N VAL A 382 SHEET 3 AD 5 THR A 402 SER A 410 -1 O THR A 402 N VAL A 373 SHEET 4 AD 5 SER A 417 ILE A 426 -1 O ILE A 418 N ILE A 409 SHEET 5 AD 5 TYR A 431 ASN A 433 -1 O GLU A 432 N LEU A 425 LINK FE FE A1446 OD1 ASP A 295 1555 1555 2.42 LINK FE FE A1446 OD2 ASP A 295 1555 1555 2.15 LINK FE FE A1446 OD1 ASP A 297 1555 1555 2.33 LINK FE FE A1446 OD1 ASP A 307 1555 1555 2.04 LINK FE FE A1446 OE1 GLU A 421 1555 1555 2.45 LINK FE FE A1447 OE2 GLU A 421 1555 1555 2.09 LINK FE FE A1447 OD2 ASP A 307 1555 1555 2.70 LINK FE FE A1447 NE2 HIS A 371 1555 1555 2.20 LINK FE FE A1447 OE2 GLU A 406 1555 1555 2.12 CISPEP 1 ASN A 275 PRO A 276 0 4.67 CISPEP 2 TRP A 379 PRO A 380 0 1.85 SITE 1 AC1 5 ASP A 295 ASP A 297 ASP A 307 GLU A 421 SITE 2 AC1 5 FE A1447 SITE 1 AC2 5 ASP A 307 HIS A 371 GLU A 406 GLU A 421 SITE 2 AC2 5 FE A1446 CRYST1 116.850 116.850 133.430 90.00 90.00 120.00 P 63 2 2 12 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 0.008558 0.004941 0.000000 0.00000 SCALE2 0.000000 0.009882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007495 0.00000