HEADER TRANSFERASE 15-AUG-11 3TFJ TITLE DMSP-DEPENDENT DEMETHYLASE FROM P. UBIQUE - WITH COFACTOR THF 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 3TFJ 1 REMARK LINK REVDAT 2 29-FEB-12 3TFJ 1 JRNL REVDAT 1 28-DEC-11 3TFJ 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) : 36.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 94862 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) : 0.128 REMARK 3 R VALUE (WORKING SET) : 0.126 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.500 REMARK 3 FREE R VALUE TEST SET COUNT : 2389 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) : 6367 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.1190 REMARK 3 BIN FREE R VALUE SET COUNT : 158 REMARK 3 BIN FREE R VALUE : 0.2100 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 : 86 REMARK 3 SOLVENT ATOMS : 733 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.63000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : -0.08000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.42000 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): 0.078 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.048 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.966 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6410 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4487 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8691 ; 1.949 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11035 ; 1.100 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 820 ; 7.559 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 305 ;40.939 ;25.344 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1207 ;15.398 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;20.161 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 918 ; 0.141 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7190 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1294 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3817 ; 2.235 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1557 ; 0.793 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6209 ; 3.312 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2593 ; 4.818 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2441 ; 6.777 ; 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): 10897 ; 2.062 ; 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 3TFJ 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_1000067418. 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 : 97287 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11700 REMARK 200 FOR THE DATA SET : 17.4000 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 (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.23200 REMARK 200 FOR SHELL : 5.000 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 (%): 46.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 MM HEPES, 325 MM NACL, 20% PEG. PEG REMARK 280 INCREASED TO 30% FOR CRYO. SOAKED WITH THF UNDER ANAEROBIC REMARK 280 CONDITIONS. , PH 6.8, MICROBATCH 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 60.83250 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: 7910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 B 686 O HOH B 726 1.62 REMARK 500 O HOH B 625 O HOH B 756 1.65 REMARK 500 O HOH B 652 O HOH B 727 1.75 REMARK 500 O HOH A 604 O HOH B 558 1.78 REMARK 500 O HOH B 565 O HOH B 727 1.87 REMARK 500 O HOH A 520 O HOH B 559 1.90 REMARK 500 O HOH B 551 O HOH B 726 1.90 REMARK 500 O HOH A 436 O HOH A 621 1.95 REMARK 500 O HOH B 379 O HOH B 617 1.98 REMARK 500 NZ LYS B 341 O HOH B 667 2.03 REMARK 500 OE1 THG B 370 O HOH B 671 2.08 REMARK 500 O HOH B 447 O HOH B 592 2.12 REMARK 500 NE2 HIS B 329 O HOH B 526 2.14 REMARK 500 O HOH A 489 O HOH A 597 2.16 REMARK 500 O HOH A 604 O HOH B 625 2.17 REMARK 500 OE2 GLU A 116 O HOH A 663 2.17 REMARK 500 OE1 GLU B 186 O HOH B 693 2.18 REMARK 500 OH TYR B 326 O HOH B 712 2.19 REMARK 500 OE1 THG A 370 O HOH A 670 2.19 REMARK 500 OD1 ASP B 298 O ASN B 360 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 B 83 CG ARG B 83 CD -0.186 REMARK 500 GLU B 278 CB GLU B 278 CG 0.117 REMARK 500 GLU B 320 CB GLU B 320 CG -0.146 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 ARG A 20 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 GLU A 278 CA - CB - CG ANGL. DEV. = 17.4 DEGREES REMARK 500 ARG A 293 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 92 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 LEU B 285 CA - CB - CG ANGL. DEV. = 14.2 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 -123.48 -126.65 REMARK 500 ASN A 249 -76.64 -96.54 REMARK 500 GLU A 278 -102.07 18.87 REMARK 500 GLU A 278 -93.53 6.68 REMARK 500 GLU A 313 -9.93 -57.26 REMARK 500 SER A 347 -15.34 93.76 REMARK 500 ASN A 355 -93.08 60.08 REMARK 500 ASP A 356 23.57 -144.56 REMARK 500 LYS B 2 -72.45 -152.42 REMARK 500 PHE B 41 72.61 -119.54 REMARK 500 HIS B 54 -125.96 -121.19 REMARK 500 ALA B 124 -168.88 -73.70 REMARK 500 ASN B 249 -76.88 -93.03 REMARK 500 SER B 347 -12.77 89.76 REMARK 500 ASN B 355 -124.91 57.53 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 278 135.45 REMARK 500 LYS A 277 GLU A 278 142.13 REMARK 500 MET B 1 LYS B 2 143.27 REMARK 500 MET B 1 LYS B 2 142.76 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 373 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 36 O REMARK 620 2 ASP A 59 OD2 113.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 373 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU B 36 O REMARK 620 2 ASP B 59 OD2 114.0 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 THG A 370 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 371 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 372 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 373 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THG B 370 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 371 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 372 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 373 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: 3TFI RELATED DB: PDB REMARK 900 DMSP-DEPENDENT DEMETHYLASE FROM P. UBIQUE - WITH SUBSTRATE DMSP DBREF 3TFJ A 1 369 UNP Q4FP21 Q4FP21_PELUB 1 369 DBREF 3TFJ 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 THG A 370 32 HET ACT A 371 4 HET GOL A 372 6 HET NA A 373 1 HET THG B 370 32 HET ACT B 371 4 HET GOL B 372 6 HET NA B 373 1 HETNAM THG (6S)-5,6,7,8-TETRAHYDROFOLATE HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 THG 2(C19 H23 N7 O6) FORMUL 4 ACT 2(C2 H3 O2 1-) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 6 NA 2(NA 1+) FORMUL 11 HOH *733(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 GLU A 204 N ALA A 193 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 ALA A 337 N ARG A 293 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 ILE B 192 N ASP B 181 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 ILE B 339 N LYS B 291 SHEET 3 J 7 VAL B 317 SER B 327 -1 N ARG B 322 O ILE B 336 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 373 1555 1555 2.84 LINK OD2 ASP A 59 NA NA A 373 1555 1555 2.90 LINK O LEU B 36 NA NA B 373 1555 1555 2.83 LINK OD2 ASP B 59 NA NA B 373 1555 1555 2.89 CISPEP 1 LEU A 366 PRO A 367 0 -4.04 CISPEP 2 LEU B 366 PRO B 367 0 8.21 SITE 1 AC1 19 TYR A 32 GLU A 63 TYR A 95 ASP A 108 SITE 2 AC1 19 VAL A 110 SER A 122 ILE A 123 ALA A 124 SITE 3 AC1 19 PHE A 178 GLY A 196 TRP A 197 LYS A 199 SITE 4 AC1 19 GLU A 204 TYR A 206 TYR A 265 HOH A 481 SITE 5 AC1 19 HOH A 670 HOH A 735 HOH A 737 SITE 1 AC2 5 TYR A 32 TRP A 197 SER A 246 HOH A 503 SITE 2 AC2 5 HOH A 605 SITE 1 AC3 6 TYR A 247 HOH A 500 HOH A 650 HIS B 34 SITE 2 AC3 6 GLU B 147 HOH B 427 SITE 1 AC4 6 LEU A 36 LEU A 37 ASP A 59 VAL A 60 SITE 2 AC4 6 ALA A 61 ALA A 62 SITE 1 AC5 18 TYR B 32 GLU B 63 ASP B 108 VAL B 110 SITE 2 AC5 18 SER B 122 ILE B 123 ALA B 124 PHE B 178 SITE 3 AC5 18 GLY B 196 TRP B 197 LYS B 199 GLU B 204 SITE 4 AC5 18 TYR B 206 TYR B 265 HOH B 608 HOH B 658 SITE 5 AC5 18 HOH B 671 HOH B 736 SITE 1 AC6 5 TYR B 32 TRP B 197 SER B 246 HOH B 676 SITE 2 AC6 5 HOH B 748 SITE 1 AC7 8 HIS A 34 ILE A 129 GLU A 147 SER B 126 SITE 2 AC7 8 TYR B 247 HOH B 428 HOH B 483 HOH B 752 SITE 1 AC8 6 LEU B 36 LEU B 37 ASP B 59 VAL B 60 SITE 2 AC8 6 ALA B 61 ALA B 62 CRYST1 53.746 121.665 59.336 90.00 100.30 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 0.018606 0.000000 0.003382 0.00000 SCALE2 0.000000 0.008219 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017129 0.00000