HEADER TRANSFERASE 08-JAN-02 1KR5
TITLE CRYSTAL STRUCTURE OF HUMAN L-ISOASPARTYL METHYLTRANSFERASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 2.1.1.77;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PDM2X
KEYWDS ROSSMANN-FOLD DOUBLY-WOUND-ALPHA-BETA-ALPHA-SANDWICH, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR C.RYTTERSGAARD,S.C.GRIFFITH,M.R.SAWAYA,D.C.MACLAREN,S.CLARKE,
AUTHOR 2 T.O.YEATES
REVDAT 5 20-SEP-23 1KR5 1 REMARK
REVDAT 4 21-DEC-22 1KR5 1 REMARK SEQADV
REVDAT 3 24-FEB-09 1KR5 1 VERSN
REVDAT 2 27-MAR-02 1KR5 1 JRNL
REVDAT 1 08-FEB-02 1KR5 0
JRNL AUTH C.RYTTERSGAARD,S.C.GRIFFITH,M.R.SAWAYA,D.C.MACLAREN,
JRNL AUTH 2 S.CLARKE,T.O.YEATES
JRNL TITL CRYSTAL STRUCTURE OF HUMAN L-ISOASPARTYL METHYLTRANSFERASE.
JRNL REF J.BIOL.CHEM. V. 277 10642 2002
JRNL REFN ISSN 0021-9258
JRNL PMID 11792715
JRNL DOI 10.1074/JBC.M200229200
REMARK 2
REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.1
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.19
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 641174.090
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.4
REMARK 3 NUMBER OF REFLECTIONS : 11959
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 SET) : 0.221
REMARK 3 FREE R VALUE : 0.264
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.100
REMARK 3 FREE R VALUE TEST SET COUNT : 731
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.80
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1334
REMARK 3 BIN R VALUE (WORKING SET) : 0.3180
REMARK 3 BIN FREE R VALUE : 0.3450
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.80
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 97
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1634
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 26
REMARK 3 SOLVENT ATOMS : 64
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 15.40
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.10
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.54000
REMARK 3 B22 (A**2) : -17.41000
REMARK 3 B33 (A**2) : 14.87000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 5.86000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31
REMARK 3 ESD FROM SIGMAA (A) : 0.37
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.39
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.44
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.007
REMARK 3 BOND ANGLES (DEGREES) : 1.400
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.950
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 1.290 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.010 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.020 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.840 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.37
REMARK 3 BSOL : 63.45
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : SAH.PAR
REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 4 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : SAH.TOP
REMARK 3 TOPOLOGY FILE 3 : WATER.TOP
REMARK 3 TOPOLOGY FILE 4 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1KR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-02.
REMARK 100 THE DEPOSITION ID IS D_1000015256.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 08-MAR-01
REMARK 200 TEMPERATURE (KELVIN) : 118
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X8C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.100
REMARK 200 MONOCHROMATOR : MIRROR
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12501
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100
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 (%) : 94.7
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.07400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18
REMARK 200 COMPLETENESS FOR SHELL (%) : 75.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.25600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: EPMR
REMARK 200 STARTING MODEL: PDB ENTRY 1JG1
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.99
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MAGNESIUM ACETATE,
REMARK 280 CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
REMARK 280 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 26.84900
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 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 ALA A 1
REMARK 465 TRP A 2
REMARK 465 LYS A 3
REMARK 465 SER A 4
REMARK 465 GLY A 5
REMARK 465 GLY A 6
REMARK 465 TRP A 225
REMARK 465 LYS A 226
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 18 CG CD CE NZ
REMARK 470 LYS A 41 CG CD CE NZ
REMARK 470 LYS A 104 CG CD CE NZ
REMARK 470 LYS A 112 CG CD CE NZ
REMARK 470 LYS A 220 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 LYS A 23 10.96 -141.09
REMARK 500 THR A 34 79.12 -111.92
REMARK 500 LEU A 75 42.49 -104.37
REMARK 500 TYR A 146 75.20 -153.40
REMARK 500 LEU A 207 -71.48 -103.92
REMARK 500 THR A 216 -161.41 -129.85
REMARK 500 SER A 223 -71.63 -104.14
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
DBREF 1KR5 A 1 226 UNP P22061 PIMT_HUMAN 1 226
SEQADV 1KR5 VAL A 119 UNP P22061 ILE 119 VARIANT
SEQRES 1 A 226 ALA TRP LYS SER GLY GLY ALA SER HIS SER GLU LEU ILE
SEQRES 2 A 226 HIS ASN LEU ARG LYS ASN GLY ILE ILE LYS THR ASP LYS
SEQRES 3 A 226 VAL PHE GLU VAL MET LEU ALA THR ASP ARG SER HIS TYR
SEQRES 4 A 226 ALA LYS CYS ASN PRO TYR MET ASP SER PRO GLN SER ILE
SEQRES 5 A 226 GLY PHE GLN ALA THR ILE SER ALA PRO HIS MET HIS ALA
SEQRES 6 A 226 TYR ALA LEU GLU LEU LEU PHE ASP GLN LEU HIS GLU GLY
SEQRES 7 A 226 ALA LYS ALA LEU ASP VAL GLY SER GLY SER GLY ILE LEU
SEQRES 8 A 226 THR ALA CYS PHE ALA ARG MET VAL GLY CYS THR GLY LYS
SEQRES 9 A 226 VAL ILE GLY ILE ASP HIS ILE LYS GLU LEU VAL ASP ASP
SEQRES 10 A 226 SER VAL ASN ASN VAL ARG LYS ASP ASP PRO THR LEU LEU
SEQRES 11 A 226 SER SER GLY ARG VAL GLN LEU VAL VAL GLY ASP GLY ARG
SEQRES 12 A 226 MET GLY TYR ALA GLU GLU ALA PRO TYR ASP ALA ILE HIS
SEQRES 13 A 226 VAL GLY ALA ALA ALA PRO VAL VAL PRO GLN ALA LEU ILE
SEQRES 14 A 226 ASP GLN LEU LYS PRO GLY GLY ARG LEU ILE LEU PRO VAL
SEQRES 15 A 226 GLY PRO ALA GLY GLY ASN GLN MET LEU GLU GLN TYR ASP
SEQRES 16 A 226 LYS LEU GLN ASP GLY SER ILE LYS MET LYS PRO LEU MET
SEQRES 17 A 226 GLY VAL ILE TYR VAL PRO LEU THR ASP LYS GLU LYS GLN
SEQRES 18 A 226 TRP SER ARG TRP LYS
HET SAH A 300 26
HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE
FORMUL 2 SAH C14 H20 N6 O5 S
FORMUL 3 HOH *64(H2 O)
HELIX 1 1 SER A 8 ASN A 19 1 12
HELIX 2 2 THR A 24 THR A 34 1 11
HELIX 3 3 ASP A 35 TYR A 39 5 5
HELIX 4 4 ALA A 60 LEU A 71 1 12
HELIX 5 5 PHE A 72 HIS A 76 5 5
HELIX 6 6 GLY A 89 VAL A 99 1 11
HELIX 7 7 ILE A 111 ASP A 126 1 16
HELIX 8 8 PRO A 127 SER A 132 1 6
HELIX 9 9 ASP A 141 GLY A 145 5 5
HELIX 10 10 TYR A 146 ALA A 150 5 5
HELIX 11 11 PRO A 165 GLN A 171 1 7
HELIX 12 12 ASP A 217 TRP A 222 1 6
SHEET 1 A 2 GLN A 50 SER A 51 0
SHEET 2 A 2 THR A 57 ILE A 58 -1 O ILE A 58 N GLN A 50
SHEET 1 B 7 VAL A 135 VAL A 139 0
SHEET 2 B 7 LYS A 104 ASP A 109 1 N GLY A 107 O GLN A 136
SHEET 3 B 7 LYS A 80 VAL A 84 1 N ASP A 83 O ILE A 106
SHEET 4 B 7 TYR A 152 VAL A 157 1 O HIS A 156 N VAL A 84
SHEET 5 B 7 LEU A 172 VAL A 182 1 O LYS A 173 N TYR A 152
SHEET 6 B 7 GLN A 189 LYS A 196 -1 O TYR A 194 N LEU A 178
SHEET 7 B 7 ILE A 202 VAL A 210 -1 O VAL A 210 N GLN A 189
CISPEP 1 ALA A 150 PRO A 151 0 -0.79
SITE 1 AC1 23 ALA A 56 THR A 57 ILE A 58 SER A 59
SITE 2 AC1 23 HIS A 64 GLY A 85 SER A 86 GLY A 87
SITE 3 AC1 23 SER A 88 ASP A 109 HIS A 110 LEU A 114
SITE 4 AC1 23 GLY A 140 ASP A 141 GLY A 142 ARG A 143
SITE 5 AC1 23 GLY A 158 PRO A 214 LEU A 215 THR A 216
SITE 6 AC1 23 GLN A 221 HOH A 301 HOH A 304
CRYST1 48.007 53.698 49.003 90.00 115.60 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 0.020830 0.000000 0.009980 0.00000
SCALE2 0.000000 0.018623 0.000000 0.00000
SCALE3 0.000000 0.000000 0.022628 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
