HEADER TRANSFERASE 30-JUL-09 3IHT TITLE CRYSTAL STRUCTURE OF S-ADENOSYL-L-METHIONINE METHYL TRANSFERASE TITLE 2 (YP_165822.1) FROM SILICIBACTER POMEROYI DSS-3 AT 1.80 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-ADENOSYL-L-METHIONINE METHYL TRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RUEGERIA POMEROYI DSS-3; SOURCE 3 ORGANISM_TAXID: 246200; SOURCE 4 GENE: SPO0562, YP_165822.1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS YP_165822.1, S-ADENOSYL-L-METHIONINE METHYL TRANSFERASE, STRUCTURAL KEYWDS 2 GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN KEYWDS 3 STRUCTURE INITIATIVE, PSI-2, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 01-FEB-23 3IHT 1 REMARK SEQADV REVDAT 4 24-JUL-19 3IHT 1 REMARK LINK REVDAT 3 01-NOV-17 3IHT 1 REMARK REVDAT 2 13-JUL-11 3IHT 1 VERSN REVDAT 1 25-AUG-09 3IHT 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF S-ADENOSYL-L-METHIONINE METHYL JRNL TITL 2 TRANSFERASE (YP_165822.1) FROM SILICIBACTER POMEROYI DSS-3 JRNL TITL 3 AT 1.80 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0053 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 43956 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2213 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3021 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 176 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2518 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 309 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 26.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.48000 REMARK 3 B22 (A**2) : -0.48000 REMARK 3 B33 (A**2) : 0.72000 REMARK 3 B12 (A**2) : -0.24000 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): 0.100 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.095 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.190 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2740 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1921 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3739 ; 1.379 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4655 ; 0.894 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 356 ; 5.225 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 136 ;35.772 ;22.426 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 457 ;13.046 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;15.392 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 409 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3105 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 582 ; 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): 1670 ; 0.820 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 676 ; 0.209 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2695 ; 1.467 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1070 ; 2.183 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1025 ; 3.536 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 173 6 REMARK 3 1 B 1 B 173 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 1 A (A): 1945 ; 0.560 ; 5.000 REMARK 3 LOOSE THERMAL 1 A (A**2): 1945 ; 5.850 ;10.000 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 11 A 173 REMARK 3 RESIDUE RANGE : A 200 A 200 REMARK 3 ORIGIN FOR THE GROUP (A): 11.6119 50.6645 8.9425 REMARK 3 T TENSOR REMARK 3 T11: 0.0081 T22: 0.0036 REMARK 3 T33: 0.0040 T12: -0.0015 REMARK 3 T13: -0.0057 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: 0.9584 L22: 0.9511 REMARK 3 L33: 0.6837 L12: 0.0654 REMARK 3 L13: -0.4048 L23: 0.0617 REMARK 3 S TENSOR REMARK 3 S11: -0.0354 S12: -0.0106 S13: 0.0258 REMARK 3 S21: 0.0262 S22: 0.0089 S23: -0.0158 REMARK 3 S31: -0.0369 S32: 0.0264 S33: 0.0264 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 : B 11 B 172 REMARK 3 ORIGIN FOR THE GROUP (A): -4.1068 21.8845 7.6307 REMARK 3 T TENSOR REMARK 3 T11: 0.0341 T22: 0.0644 REMARK 3 T33: 0.0829 T12: 0.0111 REMARK 3 T13: 0.0359 T23: -0.0364 REMARK 3 L TENSOR REMARK 3 L11: 2.2413 L22: 0.6311 REMARK 3 L33: 0.7891 L12: 0.5006 REMARK 3 L13: 0.2498 L23: 0.0678 REMARK 3 S TENSOR REMARK 3 S11: -0.0610 S12: 0.1756 S13: -0.1951 REMARK 3 S21: 0.0633 S22: 0.0355 S23: 0.0326 REMARK 3 S31: -0.0216 S32: -0.0050 S33: 0.0255 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR REMARK 3 SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE REMARK 3 OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO REMARK 3 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. REMARK 3 4. S-ADENOSYLMETHIONINE (SAM) WAS MODELED BASED ON STRUCTURAL REMARK 3 HOMOLOGY AND DENSITY. THE SAM IN THE SECOND DIMER IS IS VERY REMARK 3 WEAK AND NOT MODELLED 5. GLYCEROL AND NICKEL MODELED ARE PRESENT REMARK 3 IN CRYSTALLIZATION CONDITIONS. REMARK 4 REMARK 4 3IHT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054428. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-09 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 : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91837,0.97934,0.97922 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : FLAT COLLIMATING MIRROR, TOROID REMARK 200 FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43986 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 29.934 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.73500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20.0000% GLYCEROL, 0.1600M MG(OAC)2, REMARK 280 16.0000% PEG-8000, 0.1M CACODYLATE PH 6.5, NANODROP, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 57.20867 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 28.60433 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.60433 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 57.20867 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 179 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 0 REMARK 465 MSE A 1 REMARK 465 ARG A 2 REMARK 465 GLU A 3 REMARK 465 MSE A 4 REMARK 465 GLN A 5 REMARK 465 ILE A 6 REMARK 465 MSE A 7 REMARK 465 SER A 8 REMARK 465 GLN A 9 REMARK 465 PRO A 10 REMARK 465 GLY B 0 REMARK 465 MSE B 1 REMARK 465 ARG B 2 REMARK 465 GLU B 3 REMARK 465 MSE B 4 REMARK 465 GLN B 5 REMARK 465 ILE B 6 REMARK 465 MSE B 7 REMARK 465 SER B 8 REMARK 465 GLN B 9 REMARK 465 PRO B 10 REMARK 465 GLY B 115 REMARK 465 GLY B 173 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 21 CZ NH1 NH2 REMARK 470 GLU A 100 CD OE1 OE2 REMARK 470 ARG A 118 CD NE CZ NH1 NH2 REMARK 470 GLU B 100 CD OE1 OE2 REMARK 470 ARG B 118 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 123 CZ NH1 NH2 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 B 14 NE - CZ - NH2 ANGL. DEV. = -3.7 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 ALA A 74 39.90 -145.58 REMARK 500 ALA B 104 58.98 -90.37 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 NI A 174 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 151 OE2 REMARK 620 2 HOH A 342 O 122.1 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 SAM A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 174 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 175 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 176 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 392348 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING REMARK 999 ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3IHT A 1 173 UNP Q5LVY3 Q5LVY3_SILPO 1 173 DBREF 3IHT B 1 173 UNP Q5LVY3 Q5LVY3_SILPO 1 173 SEQADV 3IHT GLY A 0 UNP Q5LVY3 EXPRESSION TAG SEQADV 3IHT GLY B 0 UNP Q5LVY3 EXPRESSION TAG SEQRES 1 A 174 GLY MSE ARG GLU MSE GLN ILE MSE SER GLN PRO GLU GLN SEQRES 2 A 174 SER ARG LEU ASP LEU PHE ILE ASP ARG MSE VAL SER GLN SEQRES 3 A 174 ARG ALA CYS LEU GLU HIS ALA ILE ALA GLN THR ALA GLY SEQRES 4 A 174 LEU SER GLY PRO VAL TYR GLU LEU GLY LEU GLY ASN GLY SEQRES 5 A 174 ARG THR TYR HIS HIS LEU ARG GLN HIS VAL GLN GLY ARG SEQRES 6 A 174 GLU ILE TYR VAL PHE GLU ARG ALA VAL ALA SER HIS PRO SEQRES 7 A 174 ASP SER THR PRO PRO GLU ALA GLN LEU ILE LEU GLY ASP SEQRES 8 A 174 ILE ARG GLU THR LEU PRO ALA THR LEU GLU ARG PHE GLY SEQRES 9 A 174 ALA THR ALA SER LEU VAL HIS ALA ASP LEU GLY GLY HIS SEQRES 10 A 174 ASN ARG GLU LYS ASN ASP ARG PHE ALA ARG LEU ILE SER SEQRES 11 A 174 PRO LEU ILE GLU PRO HIS LEU ALA GLN GLY GLY LEU MSE SEQRES 12 A 174 VAL SER SER ASP ARG MSE TYR PHE GLU GLY LEU GLU GLU SEQRES 13 A 174 LEU PRO LEU PRO PRO GLY ALA VAL VAL GLY ARG CYS PHE SEQRES 14 A 174 ILE TYR ARG ARG GLY SEQRES 1 B 174 GLY MSE ARG GLU MSE GLN ILE MSE SER GLN PRO GLU GLN SEQRES 2 B 174 SER ARG LEU ASP LEU PHE ILE ASP ARG MSE VAL SER GLN SEQRES 3 B 174 ARG ALA CYS LEU GLU HIS ALA ILE ALA GLN THR ALA GLY SEQRES 4 B 174 LEU SER GLY PRO VAL TYR GLU LEU GLY LEU GLY ASN GLY SEQRES 5 B 174 ARG THR TYR HIS HIS LEU ARG GLN HIS VAL GLN GLY ARG SEQRES 6 B 174 GLU ILE TYR VAL PHE GLU ARG ALA VAL ALA SER HIS PRO SEQRES 7 B 174 ASP SER THR PRO PRO GLU ALA GLN LEU ILE LEU GLY ASP SEQRES 8 B 174 ILE ARG GLU THR LEU PRO ALA THR LEU GLU ARG PHE GLY SEQRES 9 B 174 ALA THR ALA SER LEU VAL HIS ALA ASP LEU GLY GLY HIS SEQRES 10 B 174 ASN ARG GLU LYS ASN ASP ARG PHE ALA ARG LEU ILE SER SEQRES 11 B 174 PRO LEU ILE GLU PRO HIS LEU ALA GLN GLY GLY LEU MSE SEQRES 12 B 174 VAL SER SER ASP ARG MSE TYR PHE GLU GLY LEU GLU GLU SEQRES 13 B 174 LEU PRO LEU PRO PRO GLY ALA VAL VAL GLY ARG CYS PHE SEQRES 14 B 174 ILE TYR ARG ARG GLY MODRES 3IHT MSE A 22 MET SELENOMETHIONINE MODRES 3IHT MSE A 142 MET SELENOMETHIONINE MODRES 3IHT MSE A 148 MET SELENOMETHIONINE MODRES 3IHT MSE B 22 MET SELENOMETHIONINE MODRES 3IHT MSE B 142 MET SELENOMETHIONINE MODRES 3IHT MSE B 148 MET SELENOMETHIONINE HET MSE A 22 13 HET MSE A 142 8 HET MSE A 148 8 HET MSE B 22 8 HET MSE B 142 8 HET MSE B 148 8 HET SAM A 200 27 HET NI A 174 1 HET NI A 175 1 HET GOL A 176 6 HETNAM MSE SELENOMETHIONINE HETNAM SAM S-ADENOSYLMETHIONINE HETNAM NI NICKEL (II) ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 3 SAM C15 H22 N6 O5 S FORMUL 4 NI 2(NI 2+) FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *309(H2 O) HELIX 1 1 SER A 13 THR A 36 1 24 HELIX 2 2 GLY A 51 VAL A 61 1 11 HELIX 3 3 HIS A 76 THR A 80 5 5 HELIX 4 4 PRO A 82 ALA A 84 5 3 HELIX 5 5 ASP A 90 GLY A 103 1 14 HELIX 6 6 ASN A 117 GLU A 133 1 17 HELIX 7 7 SER B 13 THR B 36 1 24 HELIX 8 8 GLY B 51 VAL B 61 1 11 HELIX 9 9 HIS B 76 THR B 80 5 5 HELIX 10 10 PRO B 82 ALA B 84 5 3 HELIX 11 11 ASP B 90 GLY B 103 1 14 HELIX 12 12 ASN B 117 GLU B 133 1 17 SHEET 1 A 7 LEU A 86 LEU A 88 0 SHEET 2 A 7 ILE A 66 GLU A 70 1 N VAL A 68 O ILE A 87 SHEET 3 A 7 VAL A 43 LEU A 46 1 N GLU A 45 O TYR A 67 SHEET 4 A 7 ALA A 106 ALA A 111 1 O HIS A 110 N LEU A 46 SHEET 5 A 7 LEU A 136 SER A 144 1 O ALA A 137 N ALA A 106 SHEET 6 A 7 PHE A 168 ARG A 171 -1 O TYR A 170 N MSE A 142 SHEET 7 A 7 GLU A 154 LEU A 156 -1 N LEU A 156 O ILE A 169 SHEET 1 B 7 LEU B 86 LEU B 88 0 SHEET 2 B 7 ILE B 66 GLU B 70 1 N VAL B 68 O ILE B 87 SHEET 3 B 7 VAL B 43 LEU B 46 1 N GLU B 45 O PHE B 69 SHEET 4 B 7 ALA B 106 ALA B 111 1 O LEU B 108 N TYR B 44 SHEET 5 B 7 LEU B 136 SER B 144 1 O ALA B 137 N ALA B 106 SHEET 6 B 7 PHE B 168 ARG B 171 -1 O PHE B 168 N SER B 144 SHEET 7 B 7 GLU B 154 GLU B 155 -1 N GLU B 154 O ARG B 171 LINK C ARG A 21 N MSE A 22 1555 1555 1.34 LINK C MSE A 22 N VAL A 23 1555 1555 1.33 LINK C LEU A 141 N MSE A 142 1555 1555 1.34 LINK C MSE A 142 N VAL A 143 1555 1555 1.33 LINK C ARG A 147 N MSE A 148 1555 1555 1.34 LINK C MSE A 148 N TYR A 149 1555 1555 1.33 LINK C ARG B 21 N MSE B 22 1555 1555 1.33 LINK C MSE B 22 N VAL B 23 1555 1555 1.33 LINK C LEU B 141 N MSE B 142 1555 1555 1.33 LINK C MSE B 142 N VAL B 143 1555 1555 1.33 LINK C ARG B 147 N MSE B 148 1555 1555 1.34 LINK C MSE B 148 N TYR B 149 1555 1555 1.33 LINK OE2 GLU A 151 NI NI A 174 1555 1555 1.95 LINK NI NI A 174 O HOH A 342 1555 1555 2.51 LINK NI NI A 175 O HOH A 342 1555 1555 2.30 SITE 1 AC1 20 GLY A 47 LEU A 48 GLY A 49 GLY A 51 SITE 2 AC1 20 ARG A 52 THR A 53 GLU A 70 ARG A 71 SITE 3 AC1 20 GLY A 89 ASP A 90 ILE A 91 ASP A 112 SITE 4 AC1 20 GLY A 114 PHE A 124 HOH A 188 HOH A 283 SITE 5 AC1 20 HOH A 312 HOH A 325 HOH A 347 HOH A 368 SITE 1 AC2 5 HIS A 76 GLU A 151 NI A 175 HOH A 342 SITE 2 AC2 5 HIS B 116 SITE 1 AC3 2 NI A 174 HOH A 342 SITE 1 AC4 7 HIS A 31 ARG A 147 GLU A 155 PRO A 160 SITE 2 AC4 7 HOH A 238 HOH A 266 HOH A 373 CRYST1 97.568 97.568 85.813 90.00 90.00 120.00 P 32 2 1 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 0.010249 0.005917 0.000000 0.00000 SCALE2 0.000000 0.011835 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011653 0.00000