HEADER TRANSFERASE 15-AUG-11 3TFI TITLE DMSP-DEPENDENT DEMETHYLASE FROM P. UBIQUE - WITH SUBSTRATE DMSP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GCVT-LIKE AMINOMETHYLTRANSFERASE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.1.2.10; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDATUS PELAGIBACTER UBIQUE; SOURCE 3 ORGANISM_TAXID: 335992; SOURCE 4 STRAIN: HTCC1062; SOURCE 5 GENE: DMDA, SAR11_0246; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TOP10F'; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PABX101 KEYWDS DEMETHYLASE, THF, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.J.SCHULLER,C.R.REISCH,M.A.MORAN,W.B.WHITMAN,W.N.LANZILOTTA REVDAT 3 13-SEP-23 3TFI 1 REMARK LINK REVDAT 2 29-FEB-12 3TFI 1 JRNL REVDAT 1 28-DEC-11 3TFI 0 JRNL AUTH D.J.SCHULLER,C.R.REISCH,M.A.MORAN,W.B.WHITMAN,W.N.LANZILOTTA JRNL TITL STRUCTURES OF DIMETHYLSULFONIOPROPIONATE-DEPENDENT JRNL TITL 2 DEMETHYLASE FROM THE MARINE ORGANISM PELAGABACTER UBIQUE. JRNL REF PROTEIN SCI. V. 21 289 2012 JRNL REFN ISSN 0961-8368 JRNL PMID 22162093 JRNL DOI 10.1002/PRO.2015 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 94015 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) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.500 REMARK 3 FREE R VALUE TEST SET COUNT : 2369 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7084 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.1020 REMARK 3 BIN FREE R VALUE SET COUNT : 183 REMARK 3 BIN FREE R VALUE : 0.2000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5898 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 677 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.98000 REMARK 3 B22 (A**2) : -0.35000 REMARK 3 B33 (A**2) : -0.18000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.30000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.081 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.843 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6322 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4435 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8562 ; 1.968 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10916 ; 1.096 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 815 ; 7.528 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 304 ;40.701 ;25.362 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1202 ;15.775 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;21.156 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 912 ; 0.142 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7069 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1251 ; 0.001 ; 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): 3790 ; 2.287 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1550 ; 0.822 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6164 ; 3.362 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2532 ; 4.940 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2360 ; 6.987 ; 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): 10757 ; 2.132 ; 3.000 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 : 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 3TFI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067417. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) COOLED REMARK 200 WITH LN2 REMARK 200 OPTICS : VERTICAL FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 96714 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 23.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.15100 REMARK 200 FOR SHELL : 10.00 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: PDB ENTRIES 1WOO, 1V5V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 MM HEPES, 325 MM NACL, 20% PEG. PEG REMARK 280 INCREASED TO 30% FOR CRYO. SOAKED WITH DMSP, PH 6.8, MICROBATCH REMARK 280 UNDER OIL, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 60.99600 REMARK 290 SMTRY3 2 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: 5540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 488 O HOH A 595 1.71 REMARK 500 O HOH A 546 O HOH B 584 1.76 REMARK 500 OG SER A 14 O HOH A 595 1.86 REMARK 500 O HOH A 627 O HOH B 583 1.86 REMARK 500 OH TYR A 48 O HOH A 474 1.90 REMARK 500 ND2 ASN B 273 O HOH B 615 1.94 REMARK 500 O THR A 305 O HOH A 546 2.00 REMARK 500 NZ LYS A 23 O HOH A 434 2.02 REMARK 500 CB PRO B 367 O HOH B 678 2.05 REMARK 500 OG SER B 14 O HOH B 714 2.15 REMARK 500 OH TYR A 48 OE1 GLU A 241 2.18 REMARK 500 O HOH B 576 O HOH B 667 2.18 REMARK 500 CE MET B 1 O HOH B 469 2.18 REMARK 500 OE2 GLU A 278 O HOH A 381 2.19 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 ARG A 83 CG ARG A 83 CD -0.209 REMARK 500 ARG B 83 CG ARG B 83 CD -0.199 REMARK 500 GLU B 320 CB GLU B 320 CG -0.137 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 LEU A 275 CB - CG - CD1 ANGL. DEV. = 11.1 DEGREES REMARK 500 GLU A 278 CA - CB - CG ANGL. DEV. = 17.0 DEGREES REMARK 500 ARG A 293 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 MET A 338 CB - CG - SD ANGL. DEV. = 18.4 DEGREES REMARK 500 ARG B 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 MET B 338 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 54 -124.28 -125.43 REMARK 500 ASP A 100 -167.48 -104.63 REMARK 500 ASN A 249 -76.46 -95.86 REMARK 500 GLU A 278 -101.96 18.93 REMARK 500 GLU A 278 -95.01 9.10 REMARK 500 SER A 347 -16.48 94.12 REMARK 500 ASN A 355 -110.30 55.08 REMARK 500 LYS B 2 -74.98 -140.22 REMARK 500 HIS B 54 -126.74 -120.18 REMARK 500 SER B 195 -177.95 -170.70 REMARK 500 ASN B 249 -75.39 -91.76 REMARK 500 SER B 347 -11.58 90.59 REMARK 500 ASN B 355 -121.06 56.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 277 GLU A 278 134.98 REMARK 500 LYS A 277 GLU A 278 140.28 REMARK 500 MET B 1 LYS B 2 143.42 REMARK 500 MET B 1 LYS B 2 144.40 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 NA A 372 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 36 O REMARK 620 2 ASP A 59 OD2 113.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 372 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU B 36 O REMARK 620 2 ASP B 59 OD2 114.4 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DQY A 370 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 371 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 372 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DQY B 370 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 371 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 372 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TFH RELATED DB: PDB REMARK 900 DMSP-DEPENDENT DEMETHYLASE FROM P. UBIQUE - APO REMARK 900 RELATED ID: 3TFJ RELATED DB: PDB REMARK 900 DMSP-DEPENDENT DEMETHYLASE FROM P. UBIQUE - WITH COFACTOR THF DBREF 3TFI A 1 369 UNP Q4FP21 Q4FP21_PELUB 1 369 DBREF 3TFI B 1 369 UNP Q4FP21 Q4FP21_PELUB 1 369 SEQRES 1 A 369 MET LYS ASN PHE SER ILE ALA LYS SER ARG ARG LEU ARG SEQRES 2 A 369 SER THR PRO TYR THR SER ARG ILE GLU LYS GLN GLY VAL SEQRES 3 A 369 THR ALA TYR THR ILE TYR ASN HIS MET LEU LEU PRO ALA SEQRES 4 A 369 ALA PHE GLY SER ILE GLU ASP SER TYR LYS HIS LEU LYS SEQRES 5 A 369 GLU HIS VAL GLN ILE TRP ASP VAL ALA ALA GLU ARG GLN SEQRES 6 A 369 VAL GLU ILE SER GLY LYS ASP SER ALA GLU LEU VAL GLN SEQRES 7 A 369 LEU MET THR CYS ARG ASP LEU SER LYS SER LYS ILE GLY SEQRES 8 A 369 ARG CYS TYR TYR CYS PRO ILE ILE ASP GLU ASN GLY ASN SEQRES 9 A 369 LEU VAL ASN ASP PRO VAL VAL LEU LYS LEU ASP GLU ASN SEQRES 10 A 369 LYS TRP TRP ILE SER ILE ALA ASP SER ASP VAL ILE PHE SEQRES 11 A 369 PHE ALA LYS GLY LEU ALA SER GLY HIS LYS PHE ASP VAL SEQRES 12 A 369 LYS ILE VAL GLU PRO VAL VAL ASP ILE MET ALA ILE GLN SEQRES 13 A 369 GLY PRO LYS SER PHE ALA LEU MET GLU LYS VAL PHE GLY SEQRES 14 A 369 LYS LYS ILE THR GLU LEU LYS PHE PHE GLY PHE ASP TYR SEQRES 15 A 369 PHE ASP PHE GLU GLY THR LYS HIS LEU ILE ALA ARG SER SEQRES 16 A 369 GLY TRP SER LYS GLN GLY GLY TYR GLU VAL TYR VAL GLU SEQRES 17 A 369 ASN THR GLN SER GLY GLN LYS LEU TYR ASP HIS LEU PHE SEQRES 18 A 369 GLU VAL GLY LYS GLU PHE ASN VAL GLY PRO GLY CYS PRO SEQRES 19 A 369 ASN LEU ILE GLU ARG ILE GLU SER ALA LEU LEU SER TYR SEQRES 20 A 369 GLY ASN ASP PHE ASP ASN ASN ASP ASN PRO PHE GLU CYS SEQRES 21 A 369 GLY PHE ASP GLN TYR VAL SER LEU ASP SER ASP ILE ASN SEQRES 22 A 369 PHE LEU GLY LYS GLU LYS LEU LYS GLU ILE LYS LEU LYS SEQRES 23 A 369 GLY PRO GLN LYS LYS LEU ARG GLY VAL LYS ILE ASP ILE SEQRES 24 A 369 LYS GLU ILE SER LEU THR GLY SER LYS ASN ILE TYR ASP SEQRES 25 A 369 GLU ASN ASN ASN VAL ILE GLY GLU LEU ARG SER ALA CYS SEQRES 26 A 369 TYR SER PRO HIS PHE GLN LYS VAL ILE GLY ILE ALA MET SEQRES 27 A 369 ILE LYS LYS SER HIS TRP GLU ALA SER GLN GLY PHE LYS SEQRES 28 A 369 ILE GLN ILE ASN ASP ASN THR ILE ASN GLY ASN VAL CYS SEQRES 29 A 369 ASP LEU PRO PHE ILE SEQRES 1 B 369 MET LYS ASN PHE SER ILE ALA LYS SER ARG ARG LEU ARG SEQRES 2 B 369 SER THR PRO TYR THR SER ARG ILE GLU LYS GLN GLY VAL SEQRES 3 B 369 THR ALA TYR THR ILE TYR ASN HIS MET LEU LEU PRO ALA SEQRES 4 B 369 ALA PHE GLY SER ILE GLU ASP SER TYR LYS HIS LEU LYS SEQRES 5 B 369 GLU HIS VAL GLN ILE TRP ASP VAL ALA ALA GLU ARG GLN SEQRES 6 B 369 VAL GLU ILE SER GLY LYS ASP SER ALA GLU LEU VAL GLN SEQRES 7 B 369 LEU MET THR CYS ARG ASP LEU SER LYS SER LYS ILE GLY SEQRES 8 B 369 ARG CYS TYR TYR CYS PRO ILE ILE ASP GLU ASN GLY ASN SEQRES 9 B 369 LEU VAL ASN ASP PRO VAL VAL LEU LYS LEU ASP GLU ASN SEQRES 10 B 369 LYS TRP TRP ILE SER ILE ALA ASP SER ASP VAL ILE PHE SEQRES 11 B 369 PHE ALA LYS GLY LEU ALA SER GLY HIS LYS PHE ASP VAL SEQRES 12 B 369 LYS ILE VAL GLU PRO VAL VAL ASP ILE MET ALA ILE GLN SEQRES 13 B 369 GLY PRO LYS SER PHE ALA LEU MET GLU LYS VAL PHE GLY SEQRES 14 B 369 LYS LYS ILE THR GLU LEU LYS PHE PHE GLY PHE ASP TYR SEQRES 15 B 369 PHE ASP PHE GLU GLY THR LYS HIS LEU ILE ALA ARG SER SEQRES 16 B 369 GLY TRP SER LYS GLN GLY GLY TYR GLU VAL TYR VAL GLU SEQRES 17 B 369 ASN THR GLN SER GLY GLN LYS LEU TYR ASP HIS LEU PHE SEQRES 18 B 369 GLU VAL GLY LYS GLU PHE ASN VAL GLY PRO GLY CYS PRO SEQRES 19 B 369 ASN LEU ILE GLU ARG ILE GLU SER ALA LEU LEU SER TYR SEQRES 20 B 369 GLY ASN ASP PHE ASP ASN ASN ASP ASN PRO PHE GLU CYS SEQRES 21 B 369 GLY PHE ASP GLN TYR VAL SER LEU ASP SER ASP ILE ASN SEQRES 22 B 369 PHE LEU GLY LYS GLU LYS LEU LYS GLU ILE LYS LEU LYS SEQRES 23 B 369 GLY PRO GLN LYS LYS LEU ARG GLY VAL LYS ILE ASP ILE SEQRES 24 B 369 LYS GLU ILE SER LEU THR GLY SER LYS ASN ILE TYR ASP SEQRES 25 B 369 GLU ASN ASN ASN VAL ILE GLY GLU LEU ARG SER ALA CYS SEQRES 26 B 369 TYR SER PRO HIS PHE GLN LYS VAL ILE GLY ILE ALA MET SEQRES 27 B 369 ILE LYS LYS SER HIS TRP GLU ALA SER GLN GLY PHE LYS SEQRES 28 B 369 ILE GLN ILE ASN ASP ASN THR ILE ASN GLY ASN VAL CYS SEQRES 29 B 369 ASP LEU PRO PHE ILE HET DQY A 370 8 HET GOL A 371 6 HET NA A 372 1 HET DQY B 370 8 HET GOL B 371 6 HET NA B 372 1 HETNAM DQY 3-(DIMETHYL-LAMBDA~4~-SULFANYL)PROPANOIC ACID HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 DQY 2(C5 H12 O2 S) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 5 NA 2(NA 1+) FORMUL 9 HOH *677(H2 O) HELIX 1 1 TYR A 17 GLU A 22 1 6 HELIX 2 2 SER A 43 HIS A 54 1 12 HELIX 3 3 ASP A 72 THR A 81 1 10 HELIX 4 4 ASP A 127 LYS A 140 1 14 HELIX 5 5 LYS A 159 GLY A 169 1 11 HELIX 6 6 LYS A 170 LEU A 175 5 6 HELIX 7 7 ASN A 209 GLY A 224 1 16 HELIX 8 8 LYS A 225 ASN A 228 5 4 HELIX 9 9 ASN A 235 SER A 242 1 8 HELIX 10 10 ASN A 256 CYS A 260 5 5 HELIX 11 11 PHE A 262 VAL A 266 5 5 HELIX 12 12 GLY A 276 GLY A 287 1 12 HELIX 13 13 SER A 342 TRP A 344 5 3 HELIX 14 14 TYR B 17 GLU B 22 1 6 HELIX 15 15 SER B 43 HIS B 54 1 12 HELIX 16 16 ASP B 72 THR B 81 1 10 HELIX 17 17 ASP B 127 LYS B 140 1 14 HELIX 18 18 LYS B 159 GLY B 169 1 11 HELIX 19 19 LYS B 170 LEU B 175 5 6 HELIX 20 20 ASN B 209 GLY B 224 1 16 HELIX 21 21 LYS B 225 ASN B 228 5 4 HELIX 22 22 ASN B 235 SER B 242 1 8 HELIX 23 23 ASN B 256 CYS B 260 5 5 HELIX 24 24 PHE B 262 VAL B 266 5 5 HELIX 25 25 GLY B 276 GLY B 287 1 12 HELIX 26 26 SER B 342 TRP B 344 5 3 SHEET 1 A 3 SER A 5 ILE A 6 0 SHEET 2 A 3 ALA B 28 TYR B 32 1 O TYR B 29 N SER A 5 SHEET 3 A 3 MET B 35 ALA B 40 -1 O LEU B 37 N THR B 30 SHEET 1 B 3 MET A 35 ALA A 40 0 SHEET 2 B 3 ALA A 28 TYR A 32 -1 N ALA A 28 O ALA A 39 SHEET 3 B 3 SER B 5 ILE B 6 1 O SER B 5 N TYR A 29 SHEET 1 C 6 PHE A 180 PHE A 185 0 SHEET 2 C 6 THR A 188 ALA A 193 -1 O ILE A 192 N ASP A 181 SHEET 3 C 6 GLY A 202 VAL A 207 -1 O TYR A 206 N LEU A 191 SHEET 4 C 6 ASP A 151 GLN A 156 -1 N MET A 153 O VAL A 205 SHEET 5 C 6 GLN A 56 ASP A 59 -1 N TRP A 58 O ALA A 154 SHEET 6 C 6 GLY A 230 GLY A 232 1 O GLY A 230 N ILE A 57 SHEET 1 D 5 CYS A 93 TYR A 95 0 SHEET 2 D 5 VAL A 110 ASP A 115 -1 O VAL A 111 N TYR A 94 SHEET 3 D 5 LYS A 118 SER A 122 -1 O TRP A 120 N LEU A 112 SHEET 4 D 5 GLN A 65 SER A 69 -1 N VAL A 66 O ILE A 121 SHEET 5 D 5 LYS A 144 VAL A 146 -1 O VAL A 146 N GLU A 67 SHEET 1 E 2 ILE A 98 ILE A 99 0 SHEET 2 E 2 LEU A 105 ASN A 107 -1 O VAL A 106 N ILE A 98 SHEET 1 F 7 LYS A 290 ILE A 297 0 SHEET 2 F 7 LYS A 332 LYS A 340 -1 O ILE A 339 N LYS A 291 SHEET 3 F 7 VAL A 317 SER A 327 -1 N ILE A 318 O LYS A 340 SHEET 4 F 7 LYS A 308 TYR A 311 -1 N LYS A 308 O LEU A 321 SHEET 5 F 7 GLY A 349 ILE A 354 -1 O LYS A 351 N TYR A 311 SHEET 6 F 7 ASN A 357 CYS A 364 -1 O ILE A 359 N ILE A 352 SHEET 7 F 7 LYS A 290 ILE A 297 -1 N GLY A 294 O CYS A 364 SHEET 1 G 6 PHE B 180 PHE B 185 0 SHEET 2 G 6 THR B 188 ALA B 193 -1 O THR B 188 N PHE B 185 SHEET 3 G 6 GLY B 202 VAL B 207 -1 O GLU B 204 N ALA B 193 SHEET 4 G 6 ASP B 151 GLN B 156 -1 N MET B 153 O VAL B 205 SHEET 5 G 6 GLN B 56 ASP B 59 -1 N GLN B 56 O GLN B 156 SHEET 6 G 6 GLY B 230 GLY B 232 1 O GLY B 230 N ILE B 57 SHEET 1 H 5 CYS B 93 TYR B 95 0 SHEET 2 H 5 VAL B 110 ASP B 115 -1 O VAL B 111 N TYR B 94 SHEET 3 H 5 LYS B 118 SER B 122 -1 O SER B 122 N VAL B 110 SHEET 4 H 5 GLN B 65 SER B 69 -1 N VAL B 66 O ILE B 121 SHEET 5 H 5 LYS B 144 VAL B 146 -1 O VAL B 146 N GLU B 67 SHEET 1 I 2 ILE B 98 ILE B 99 0 SHEET 2 I 2 LEU B 105 ASN B 107 -1 O VAL B 106 N ILE B 98 SHEET 1 J 7 LYS B 290 ILE B 297 0 SHEET 2 J 7 LYS B 332 LYS B 340 -1 O VAL B 333 N ILE B 297 SHEET 3 J 7 VAL B 317 SER B 327 -1 N CYS B 325 O ILE B 334 SHEET 4 J 7 LYS B 308 TYR B 311 -1 N LYS B 308 O LEU B 321 SHEET 5 J 7 GLY B 349 ILE B 354 -1 O LYS B 351 N TYR B 311 SHEET 6 J 7 ASN B 357 CYS B 364 -1 O ILE B 359 N ILE B 352 SHEET 7 J 7 LYS B 290 ILE B 297 -1 N GLY B 294 O CYS B 364 LINK O LEU A 36 NA NA A 372 1555 1555 2.87 LINK OD2 ASP A 59 NA NA A 372 1555 1555 2.91 LINK O LEU B 36 NA NA B 372 1555 1555 2.82 LINK OD2 ASP B 59 NA NA B 372 1555 1555 2.92 CISPEP 1 LEU A 366 PRO A 367 0 -2.42 CISPEP 2 LEU B 366 PRO B 367 0 3.03 SITE 1 AC1 8 TYR A 32 GLU A 63 TRP A 197 SER A 246 SITE 2 AC1 8 HOH A 523 HOH A 524 HOH A 628 HOH A 663 SITE 1 AC2 7 SER A 126 TYR A 247 HOH A 515 HOH A 678 SITE 2 AC2 7 HIS B 34 GLU B 147 HOH B 423 SITE 1 AC3 6 LEU A 36 LEU A 37 ASP A 59 VAL A 60 SITE 2 AC3 6 ALA A 61 ALA A 62 SITE 1 AC4 8 TYR B 32 GLU B 63 TRP B 197 SER B 246 SITE 2 AC4 8 HOH B 542 HOH B 652 HOH B 666 HOH B 703 SITE 1 AC5 8 HIS A 34 ILE A 129 GLU A 147 HOH A 398 SITE 2 AC5 8 TYR B 247 HOH B 455 HOH B 685 HOH B 709 SITE 1 AC6 6 LEU B 36 LEU B 37 ASP B 59 VAL B 60 SITE 2 AC6 6 ALA B 61 ALA B 62 CRYST1 53.752 121.992 59.373 90.00 100.17 90.00 P 1 21 1 4 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 0.018604 0.000000 0.003337 0.00000 SCALE2 0.000000 0.008197 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017111 0.00000