HEADER TRANSFERASE 26-MAR-09 3GRR
TITLE CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN S-ADENOSYL HOMOCYSTEINE AND
TITLE 2 METHANOCALDOCOCCUS JANNASCHI DIM1.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DIMETHYLADENOSINE TRANSFERASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: S-ADENOSYLMETHIONINE-6-N',N'-ADENOSYL(RRNA)
COMPND 5 DIMETHYLTRANSFERASE, 16S RRNA DIMETHYLASE;
COMPND 6 EC: 2.1.1.-;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII;
SOURCE 3 ORGANISM_COMMON: METHANOCOCCUS JANNASCHII;
SOURCE 4 ORGANISM_TAXID: 2190;
SOURCE 5 GENE: KSGA, MJ1029;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B
KEYWDS DIMETHYLADENOSINE TRANSFERASE, ROSSMANN FOLD, RIBOSOMAL ASSEMBLY S-
KEYWDS 2 ADENOSYL-L-METHIONINE, RRNA PROCESSING, RNA-BINDING, METHYL
KEYWDS 3 TRANSFERASE, METHYLTRANSFERASE, S-ADENOSYL-L-METHIONINE, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.N.SCARSDALE,F.N.MUSAYEV,J.P.RIFE
REVDAT 6 06-SEP-23 3GRR 1 REMARK
REVDAT 5 20-OCT-21 3GRR 1 REMARK SEQADV
REVDAT 4 12-NOV-14 3GRR 1 KEYWDS
REVDAT 3 13-JUL-11 3GRR 1 VERSN
REVDAT 2 07-APR-10 3GRR 1 JRNL
REVDAT 1 31-MAR-10 3GRR 0
JRNL AUTH H.C.O'FARRELL,F.N.MUSAYEV,J.N.SCARSDALE,J.P.RIFE
JRNL TITL BINDING OF ADENOSINE-BASED LIGANDS TO THE MJDIM1 RRNA
JRNL TITL 2 METHYLTRANSFERASE: IMPLICATIONS FOR REACTION MECHANISM AND
JRNL TITL 3 DRUG DESIGN.
JRNL REF BIOCHEMISTRY V. 49 2697 2010
JRNL REFN ISSN 0006-2960
JRNL PMID 20163168
JRNL DOI 10.1021/BI901875X
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH H.C.O'FARRELL,J.N.SCARSDALE,J.P.RIFE
REMARK 1 TITL CRYSTAL STRUCTURE OF KSGA, A UNIVERSALLY CONSERVED RRNA
REMARK 1 TITL 2 ADENINE DIMETHYLTRANSFERASE IN ESCHERICHIA COLI
REMARK 1 REF J.MOL.BIOL. V. 339 337 2004
REMARK 1 REFN ISSN 0022-2836
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
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) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.50
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3
REMARK 3 NUMBER OF REFLECTIONS : 24273
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) : 0.187
REMARK 3 R VALUE (WORKING SET) : 0.182
REMARK 3 FREE R VALUE : 0.234
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100
REMARK 3 FREE R VALUE TEST SET COUNT : 2733
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) : 1668
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.87
REMARK 3 BIN R VALUE (WORKING SET) : 0.2850
REMARK 3 BIN FREE R VALUE SET COUNT : 193
REMARK 3 BIN FREE R VALUE : 0.3320
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2105
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 26
REMARK 3 SOLVENT ATOMS : 211
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : 40.50
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.15
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.62000
REMARK 3 B22 (A**2) : -0.06000
REMARK 3 B33 (A**2) : 0.30000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.62000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.139
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.139
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.106
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.735
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2182 ; 0.009 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2949 ; 1.123 ; 1.984
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 264 ; 5.460 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;34.289 ;25.149
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 401 ;13.280 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;16.312 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 335 ; 0.081 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1618 ; 0.004 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1004 ; 0.185 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1530 ; 0.300 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 179 ; 0.135 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 19 ; 0.196 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.142 ; 0.200
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1376 ; 5.366 ; 4.000
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2140 ; 6.521 ; 6.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 926 ;10.157 ; 8.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 809 ;11.956 ;10.000
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 2
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 10 A 180
REMARK 3 ORIGIN FOR THE GROUP (A): 18.8112 18.8654 21.5632
REMARK 3 T TENSOR
REMARK 3 T11: -0.1109 T22: -0.1424
REMARK 3 T33: -0.1347 T12: -0.0328
REMARK 3 T13: 0.0337 T23: 0.0133
REMARK 3 L TENSOR
REMARK 3 L11: 2.8356 L22: 1.3540
REMARK 3 L33: 1.4870 L12: -0.1782
REMARK 3 L13: 0.5952 L23: 0.2422
REMARK 3 S TENSOR
REMARK 3 S11: -0.0427 S12: 0.3074 S13: 0.1044
REMARK 3 S21: -0.2460 S22: 0.0081 S23: 0.0119
REMARK 3 S31: -0.1060 S32: -0.0232 S33: 0.0346
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 192 A 272
REMARK 3 ORIGIN FOR THE GROUP (A): 42.1355 21.8545 46.8434
REMARK 3 T TENSOR
REMARK 3 T11: -0.1092 T22: -0.0964
REMARK 3 T33: -0.1655 T12: 0.0185
REMARK 3 T13: 0.0108 T23: 0.0067
REMARK 3 L TENSOR
REMARK 3 L11: 3.9448 L22: 5.1960
REMARK 3 L33: 3.7981 L12: 1.8385
REMARK 3 L13: 1.3257 L23: 1.3510
REMARK 3 S TENSOR
REMARK 3 S11: 0.1149 S12: -0.3330 S13: 0.0067
REMARK 3 S21: 0.5342 S22: -0.1490 S23: -0.0549
REMARK 3 S31: 0.0077 S32: -0.1189 S33: 0.0340
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 : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3GRR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-09.
REMARK 100 THE DEPOSITION ID IS D_1000052232.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 08-JUN-08
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.2
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : RIGAKU VARIMAX CONFOCAL OPTICS
REMARK 200 OPTICS : RIGAKU VARIMAX CONFOCAL OPTICS
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK
REMARK 200 DATA SCALING SOFTWARE : D*TREK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27022
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 17.700
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3
REMARK 200 DATA REDUNDANCY : 4.590
REMARK 200 R MERGE (I) : 0.03800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.7000
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 (%) : 88.5
REMARK 200 DATA REDUNDANCY IN SHELL : 4.45
REMARK 200 R MERGE FOR SHELL (I) : 0.34700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHENIX
REMARK 200 STARTING MODEL: 3FYD, CHAIN A
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 47.34
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000 (14-16%), 25 MM MES, 50 MM
REMARK 280 NH2SO4, 7 MM MGCL2, PH 6.2, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 293K
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 33.14950
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 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 -19
REMARK 465 GLY A -18
REMARK 465 SER A -17
REMARK 465 SER A -16
REMARK 465 HIS A -15
REMARK 465 HIS A -14
REMARK 465 HIS A -13
REMARK 465 HIS A -12
REMARK 465 HIS A -11
REMARK 465 HIS A -10
REMARK 465 SER A -9
REMARK 465 SER A -8
REMARK 465 GLY A -7
REMARK 465 LEU A -6
REMARK 465 VAL A -5
REMARK 465 PRO A -4
REMARK 465 ARG A -3
REMARK 465 GLY A -2
REMARK 465 SER A -1
REMARK 465 HIS A 0
REMARK 465 MET A 1
REMARK 465 PHE A 2
REMARK 465 LYS A 3
REMARK 465 PRO A 4
REMARK 465 LYS A 5
REMARK 465 LYS A 6
REMARK 465 LYS A 7
REMARK 465 LEU A 8
REMARK 465 GLY A 9
REMARK 465 GLY A 273
REMARK 465 ARG A 274
REMARK 465 LEU A 275
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 LYS A 16 CG CD CE NZ
REMARK 470 LYS A 70 CG CD CE NZ
REMARK 470 GLN A 105 CG CD OE1 NE2
REMARK 470 LYS A 172 CG CD CE NZ
REMARK 470 LYS A 184 CG CD CE NZ
REMARK 470 LYS A 186 CG CD CE NZ
REMARK 470 HIS A 188 CG ND1 CD2 CE1 NE2
REMARK 470 LYS A 225 CG CD CE NZ
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 ASN A 183 86.89 -150.33
REMARK 500 HIS A 188 83.99 62.33
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 300
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3FYC RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF DIM1 FROM THE THERMOPHILIC ARCHEON,
REMARK 900 METHANOCALDOCOCCUS JANNASCHI
REMARK 900 RELATED ID: 3FYD RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF DIM1 FROM THE THERMOPHILIC ARCHEON,
REMARK 900 METHANOCALDOCOCCUS JANNASCHI
REMARK 900 RELATED ID: 1QYR RELATED DB: PDB
REMARK 900 2.1 ANGSTROM CRYSTAL STRUCTURE OF KSGA: A UNIVERSALLY CONSERVED
REMARK 900 ADENOSINE DIMETHYLTRANSFERASE
REMARK 900 RELATED ID: 2H1R RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF A DIMETHYLADENOSINE TRANSFERASE FROM P.
REMARK 900 FACILPARUM
REMARK 900 RELATED ID: 1ZQ9 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN DIMETHYLADENOSINE TRANSFERASE
REMARK 900 RELATED ID: 3FUV RELATED DB: PDB
REMARK 900 APO-FORM OF T. THERMOPHILUS 16S RRNA A1518 AND A1519
REMARK 900 METHYLTRANSFERASE (KSGA) IN SPACE GROUP P43212
REMARK 900 RELATED ID: 3FUT RELATED DB: PDB
REMARK 900 APO-FORM OF T. THERMOPHILUS 16S RRNA A1518 AND A1519
REMARK 900 METHYLTRANSFERASE (KSGA) IN SPACE GROUP P21212
REMARK 900 RELATED ID: 3FUU RELATED DB: PDB
REMARK 900 T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA)
REMARK 900 IN COMPLEX WITH ADENOSINE IN SPACE GROUP P212121
REMARK 900 RELATED ID: 3FUX RELATED DB: PDB
REMARK 900 T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA)
REMARK 900 IN COMPLEX WITH 5'-METHYLTHIOADENOSINE IN SPACE GROUP P212121
REMARK 900 RELATED ID: 3FUW RELATED DB: PDB
REMARK 900 T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA)
REMARK 900 IN COMPLEX WITH 5'-METHYLTHIOADENOSINE IN SPACE GROUP P212121
REMARK 900 RELATED ID: 3GRU RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN AMP AND METHANOCALDOCOCCUS
REMARK 900 JANNASCHI DIM1
REMARK 900 RELATED ID: 3GRV RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN ADENOSINE AND
REMARK 900 METHANOCALDOCOCCUS JANNASCHI DIM1
REMARK 900 RELATED ID: 3GRY RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN S-ADENOSYL METHIONINE AND
REMARK 900 METHANOCALDOCOCCUS JANNASCHI DIM1
DBREF 3GRR A 1 275 UNP Q58435 KSGA_METJA 1 275
SEQADV 3GRR MET A -19 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR GLY A -18 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR SER A -17 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR SER A -16 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR HIS A -15 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR HIS A -14 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR HIS A -13 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR HIS A -12 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR HIS A -11 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR HIS A -10 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR SER A -9 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR SER A -8 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR GLY A -7 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR LEU A -6 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR VAL A -5 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR PRO A -4 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR ARG A -3 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR GLY A -2 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR SER A -1 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR HIS A 0 UNP Q58435 EXPRESSION TAG
SEQADV 3GRR ALA A 137 UNP Q58435 LYS 137 ENGINEERED MUTATION
SEQADV 3GRR ALA A 138 UNP Q58435 GLU 138 ENGINEERED MUTATION
SEQRES 1 A 295 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY
SEQRES 2 A 295 LEU VAL PRO ARG GLY SER HIS MET PHE LYS PRO LYS LYS
SEQRES 3 A 295 LYS LEU GLY GLN CYS PHE LEU ILE ASP LYS ASN PHE VAL
SEQRES 4 A 295 ASN LYS ALA VAL GLU SER ALA ASN LEU THR LYS ASP ASP
SEQRES 5 A 295 VAL VAL LEU GLU ILE GLY LEU GLY LYS GLY ILE LEU THR
SEQRES 6 A 295 GLU GLU LEU ALA LYS ASN ALA LYS LYS VAL TYR VAL ILE
SEQRES 7 A 295 GLU ILE ASP LYS SER LEU GLU PRO TYR ALA ASN LYS LEU
SEQRES 8 A 295 LYS GLU LEU TYR ASN ASN ILE GLU ILE ILE TRP GLY ASP
SEQRES 9 A 295 ALA LEU LYS VAL ASP LEU ASN LYS LEU ASP PHE ASN LYS
SEQRES 10 A 295 VAL VAL ALA ASN LEU PRO TYR GLN ILE SER SER PRO ILE
SEQRES 11 A 295 THR PHE LYS LEU ILE LYS ARG GLY PHE ASP LEU ALA VAL
SEQRES 12 A 295 LEU MET TYR GLN TYR GLU PHE ALA LYS ARG MET VAL ALA
SEQRES 13 A 295 ALA ALA GLY THR LYS ASP TYR GLY ARG LEU SER VAL ALA
SEQRES 14 A 295 VAL GLN SER ARG ALA ASP VAL GLU ILE VAL ALA LYS VAL
SEQRES 15 A 295 PRO PRO SER ALA PHE TYR PRO LYS PRO LYS VAL TYR SER
SEQRES 16 A 295 ALA ILE VAL LYS ILE LYS PRO ASN LYS GLY LYS TYR HIS
SEQRES 17 A 295 ILE GLU ASN GLU ASN PHE PHE ASP ASP PHE LEU ARG ALA
SEQRES 18 A 295 ILE PHE GLN HIS ARG ASN LYS SER VAL ARG LYS ALA LEU
SEQRES 19 A 295 ILE ASP SER SER LYS GLU LEU ASN TYR ASN LYS ASP GLU
SEQRES 20 A 295 MET LYS LYS ILE LEU GLU ASP PHE LEU ASN THR ASN SER
SEQRES 21 A 295 GLU ILE LYS ASN LEU ILE ASN GLU LYS VAL PHE LYS LEU
SEQRES 22 A 295 SER VAL LYS ASP ILE VAL ASN LEU SER ASN GLU PHE TYR
SEQRES 23 A 295 ARG PHE LEU GLN ASN ARG GLY ARG LEU
HET SAH A 300 26
HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE
FORMUL 2 SAH C14 H20 N6 O5 S
FORMUL 3 HOH *211(H2 O)
HELIX 1 1 ASP A 15 ALA A 26 1 12
HELIX 2 2 GLY A 42 ALA A 52 1 11
HELIX 3 3 ASP A 61 SER A 63 5 3
HELIX 4 4 LEU A 64 GLU A 73 1 10
HELIX 5 5 ASP A 89 LEU A 93 5 5
HELIX 6 6 PRO A 103 GLN A 105 5 3
HELIX 7 7 ILE A 106 GLY A 118 1 13
HELIX 8 8 TYR A 128 ALA A 136 1 9
HELIX 9 9 GLY A 144 SER A 152 1 9
HELIX 10 10 PRO A 163 SER A 165 5 3
HELIX 11 11 ASN A 191 GLN A 204 1 14
HELIX 12 12 SER A 209 SER A 217 1 9
HELIX 13 13 SER A 218 ASN A 222 5 5
HELIX 14 14 ASN A 224 ASN A 237 1 14
HELIX 15 15 ASN A 239 ASN A 247 1 9
HELIX 16 16 LYS A 249 LEU A 253 5 5
HELIX 17 17 SER A 254 ASN A 271 1 18
SHEET 1 A 2 PHE A 12 LEU A 13 0
SHEET 2 A 2 PHE A 167 TYR A 168 -1 O TYR A 168 N PHE A 12
SHEET 1 B 7 ILE A 78 TRP A 82 0
SHEET 2 B 7 LYS A 54 GLU A 59 1 N VAL A 57 O ILE A 81
SHEET 3 B 7 VAL A 33 ILE A 37 1 N GLU A 36 O TYR A 56
SHEET 4 B 7 LYS A 97 ASN A 101 1 O LYS A 97 N LEU A 35
SHEET 5 B 7 LEU A 121 GLN A 127 1 O VAL A 123 N VAL A 98
SHEET 6 B 7 SER A 175 PRO A 182 -1 O ILE A 180 N ALA A 122
SHEET 7 B 7 ALA A 154 VAL A 162 -1 N VAL A 159 O ILE A 177
CISPEP 1 TYR A 168 PRO A 169 0 -5.84
SITE 1 AC1 18 GLN A 10 PHE A 12 LEU A 13 GLY A 38
SITE 2 AC1 18 GLY A 40 ILE A 58 GLU A 59 ILE A 60
SITE 3 AC1 18 ASP A 61 LEU A 64 GLY A 83 ASP A 84
SITE 4 AC1 18 ALA A 85 ASN A 101 PRO A 103 HOH A 281
SITE 5 AC1 18 HOH A 393 HOH A 402
CRYST1 40.385 66.299 62.061 90.00 107.76 90.00 P 1 21 1 2
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 0.024762 0.000000 0.007933 0.00000
SCALE2 0.000000 0.015083 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016920 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
