PDB Short entry for 3LHD HEADER TRANSFERASE 22-JAN-10 3LHD TITLE CRYSTAL STRUCTURE OF P. ABYSSI TRNA M1A58 METHYLTRANSFERASE IN COMPLEX TITLE 2 WITH S-ADENOSYL-L-HOMOCYSTEINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SAM-DEPENDENT METHYLTRANSFERASE, PUTATIVE; COMPND 3 CHAIN: C, A, B, D; COMPND 4 EC: 2.1.1.36; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS ABYSSI; SOURCE 3 ORGANISM_TAXID: 272844; SOURCE 4 STRAIN: GE5; SOURCE 5 GENE: PAB0283; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30 KEYWDS RNA METHYLTRANSFERASE, M1A, TRMI, INTERMOLECULAR CONTACTS, REGION- KEYWDS 2 SPECIFICITY, TETRAMER, DISULFIDE BOND, HYPERTHERMOSTABILITY, KEYWDS 3 METHYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.GUELORGET,B.GOLINELLI-PIMPANEAU,J.WOUTERS,C.BARBEY REVDAT 4 06-SEP-23 3LHD 1 REMARK REVDAT 3 27-OCT-10 3LHD 1 JRNL REVDAT 2 02-JUN-10 3LHD 1 AUTHOR REMARK REVDAT 1 19-MAY-10 3LHD 0 JRNL AUTH A.GUELORGET,M.ROOVERS,V.GUERINEAU,C.BARBEY,X.LI, JRNL AUTH 2 B.GOLINELLI-PIMPANEAU JRNL TITL INSIGHTS INTO THE HYPERTHERMOSTABILITY AND UNUSUAL JRNL TITL 2 REGION-SPECIFICITY OF ARCHAEAL PYROCOCCUS ABYSSI TRNA JRNL TITL 3 M1A57/58 METHYLTRANSFERASE. JRNL REF NUCLEIC ACIDS RES. V. 38 6206 2010 JRNL REFN ISSN 0305-1048 JRNL PMID 20483913 JRNL DOI 10.1093/NAR/GKQ381 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.ROOVERS,J.WOUTERS,J.M.BUJNICKI,C.TRICOT,V.STALON, REMARK 1 AUTH 2 H.GROSJEAN,L.DROOGMANS REMARK 1 TITL A PRIMORDIAL RNA MODIFICATION ENZYME: THE CASE OF TRNA (M1A) REMARK 1 TITL 2 METHYLTRANSFERASE REMARK 1 REF NUCLEIC ACIDS RES. V. 32 465 2004 REMARK 1 REFN ISSN 0305-1048 REMARK 1 PMID 14739239 REMARK 2 REMARK 2 RESOLUTION. 2.59 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) : 2.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 36361 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) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1908 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) : 2.59 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1433 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 50.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.3330 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.3650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7950 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 104 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : 0.80000 REMARK 3 B33 (A**2) : -0.69000 REMARK 3 B12 (A**2) : 0.00000 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): 0.932 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.365 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.269 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.242 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.912 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.874 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8242 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11175 ; 1.221 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1008 ; 6.206 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 368 ;37.717 ;22.609 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1367 ;18.879 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 74 ;18.310 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1249 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6242 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3720 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 5420 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 355 ; 0.158 ; 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): 33 ; 0.225 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.160 ; 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): 5051 ; 0.494 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 8131 ; 0.951 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3191 ; 1.225 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3044 ; 2.183 ; 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 : 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 3LHD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000057279. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-SEP-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38327 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.590 REMARK 200 RESOLUTION RANGE LOW (A) : 65.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.19700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1I9G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 ACETATE, 25% PEG 4000, PH 4.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 33.01500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.69800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 63.78850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.69800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.01500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 63.78850 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -94.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, A, B, D 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 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 C 24 CG CD CE NZ REMARK 470 GLU C 37 CG CD OE1 OE2 REMARK 470 LYS C 49 CG CD CE NZ REMARK 470 GLU C 55 CG CD OE1 OE2 REMARK 470 LYS C 71 CG CD CE NZ REMARK 470 ARG C 72 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 118 CG CD OE1 OE2 REMARK 470 LYS C 182 CG CD CE NZ REMARK 470 LYS C 211 CG CD CE NZ REMARK 470 LYS C 216 CG CD CE NZ REMARK 470 LYS C 231 CG CD CE NZ REMARK 470 VAL A 22 CG1 CG2 REMARK 470 LYS A 24 CG CD CE NZ REMARK 470 ILE A 33 CG1 CG2 CD1 REMARK 470 LEU A 34 CG CD1 CD2 REMARK 470 LEU A 36 CG CD1 CD2 REMARK 470 GLU A 37 CG CD OE1 OE2 REMARK 470 ILE A 39 CG1 CG2 CD1 REMARK 470 GLU A 46 CB CG CD OE1 OE2 REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 GLU A 55 CG CD OE1 OE2 REMARK 470 LYS A 71 CG CD CE NZ REMARK 470 ARG A 72 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 75 CG CD OE1 NE2 REMARK 470 GLU A 118 CG CD OE1 OE2 REMARK 470 LYS A 182 CG CD CE NZ REMARK 470 LYS A 211 CG CD CE NZ REMARK 470 LYS A 216 CG CD CE NZ REMARK 470 LYS A 231 CG CD CE NZ REMARK 470 LYS B 24 CG CD CE NZ REMARK 470 GLU B 37 CG CD OE1 OE2 REMARK 470 LYS B 49 CG CD CE NZ REMARK 470 GLU B 55 CG CD OE1 OE2 REMARK 470 LYS B 71 CG CD CE NZ REMARK 470 GLN B 75 CG CD OE1 NE2 REMARK 470 LYS B 182 CG CD CE NZ REMARK 470 LYS B 211 CG CD CE NZ REMARK 470 LYS B 216 CG CD CE NZ REMARK 470 LYS B 231 CG CD CE NZ REMARK 470 LYS D 24 CG CD CE NZ REMARK 470 LYS D 35 CG CD CE NZ REMARK 470 GLU D 37 CG CD OE1 OE2 REMARK 470 ILE D 48 CG1 CG2 CD1 REMARK 470 LYS D 49 CG CD CE NZ REMARK 470 GLU D 55 CG CD OE1 OE2 REMARK 470 LYS D 71 CG CD CE NZ REMARK 470 GLN D 75 CG CD OE1 NE2 REMARK 470 LYS D 182 CG CD CE NZ REMARK 470 LYS D 211 CG CD CE NZ REMARK 470 LYS D 216 CG CD CE NZ REMARK 470 LYS D 231 CG CD CE NZ 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 272 O HOH B 274 2.16 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 GLN C 75 -139.86 -100.06 REMARK 500 ASP C 144 -50.56 -21.02 REMARK 500 PHE C 210 51.17 -100.63 REMARK 500 GLU C 232 -84.42 -80.90 REMARK 500 THR C 244 -70.22 -109.06 REMARK 500 PRO A 13 -2.70 -54.56 REMARK 500 LYS A 35 89.02 62.83 REMARK 500 PRO A 93 128.75 -39.75 REMARK 500 HIS D 51 37.35 -77.84 REMARK 500 PRO D 74 -71.13 -81.87 REMARK 500 ASP D 144 -55.18 -15.90 REMARK 500 PHE D 210 36.07 -99.35 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 PHE D 143 ASP D 144 149.53 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 C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH D 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3LGA RELATED DB: PDB REMARK 900 THE SAME PROTEIN CRYSTALLIZED IN ANOTHER SPACE GROUPE P31 DBREF 3LHD C 1 253 UNP Q9V1J7 Q9V1J7_PYRAB 1 253 DBREF 3LHD A 1 253 UNP Q9V1J7 Q9V1J7_PYRAB 1 253 DBREF 3LHD B 1 253 UNP Q9V1J7 Q9V1J7_PYRAB 1 253 DBREF 3LHD D 1 253 UNP Q9V1J7 Q9V1J7_PYRAB 1 253 SEQRES 1 C 253 MET ILE ARG GLU GLY ASP LYS VAL VAL LEU VAL ASP PRO SEQRES 2 C 253 ARG GLY LYS ARG TYR LEU ILE THR VAL SER LYS ARG ASP SEQRES 3 C 253 PHE HIS THR ASP LEU GLY ILE LEU LYS LEU GLU GLU ILE SEQRES 4 C 253 ILE GLY ARG ASN PHE GLY GLU ALA ILE LYS SER HIS LYS SEQRES 5 C 253 GLY HIS GLU PHE LYS ILE LEU ARG PRO ARG ILE VAL ASP SEQRES 6 C 253 TYR LEU ASP LYS MET LYS ARG GLY PRO GLN ILE VAL HIS SEQRES 7 C 253 PRO LYS ASP ALA ALA LEU ILE VAL ALA TYR ALA GLY ILE SEQRES 8 C 253 SER PRO GLY ASP PHE ILE VAL GLU ALA GLY VAL GLY SER SEQRES 9 C 253 GLY ALA LEU THR LEU PHE LEU ALA ASN ILE VAL GLY PRO SEQRES 10 C 253 GLU GLY ARG VAL VAL SER TYR GLU ILE ARG GLU ASP PHE SEQRES 11 C 253 ALA LYS LEU ALA TRP GLU ASN ILE LYS TRP ALA GLY PHE SEQRES 12 C 253 ASP ASP ARG VAL THR ILE LYS LEU LYS ASP ILE TYR GLU SEQRES 13 C 253 GLY ILE GLU GLU GLU ASN VAL ASP HIS VAL ILE LEU ASP SEQRES 14 C 253 LEU PRO GLN PRO GLU ARG VAL VAL GLU HIS ALA ALA LYS SEQRES 15 C 253 ALA LEU LYS PRO GLY GLY PHE PHE VAL ALA TYR THR PRO SEQRES 16 C 253 CYS SER ASN GLN VAL MET ARG LEU HIS GLU LYS LEU ARG SEQRES 17 C 253 GLU PHE LYS ASP TYR PHE MET LYS PRO ARG THR ILE ASN SEQRES 18 C 253 VAL LEU VAL PHE ASP GLN GLU VAL LYS LYS GLU CYS MET SEQRES 19 C 253 ARG PRO ARG THR THR ALA LEU VAL HIS THR GLY TYR ILE SEQRES 20 C 253 THR PHE ALA ARG ARG ILE SEQRES 1 A 253 MET ILE ARG GLU GLY ASP LYS VAL VAL LEU VAL ASP PRO SEQRES 2 A 253 ARG GLY LYS ARG TYR LEU ILE THR VAL SER LYS ARG ASP SEQRES 3 A 253 PHE HIS THR ASP LEU GLY ILE LEU LYS LEU GLU GLU ILE SEQRES 4 A 253 ILE GLY ARG ASN PHE GLY GLU ALA ILE LYS SER HIS LYS SEQRES 5 A 253 GLY HIS GLU PHE LYS ILE LEU ARG PRO ARG ILE VAL ASP SEQRES 6 A 253 TYR LEU ASP LYS MET LYS ARG GLY PRO GLN ILE VAL HIS SEQRES 7 A 253 PRO LYS ASP ALA ALA LEU ILE VAL ALA TYR ALA GLY ILE SEQRES 8 A 253 SER PRO GLY ASP PHE ILE VAL GLU ALA GLY VAL GLY SER SEQRES 9 A 253 GLY ALA LEU THR LEU PHE LEU ALA ASN ILE VAL GLY PRO SEQRES 10 A 253 GLU GLY ARG VAL VAL SER TYR GLU ILE ARG GLU ASP PHE SEQRES 11 A 253 ALA LYS LEU ALA TRP GLU ASN ILE LYS TRP ALA GLY PHE SEQRES 12 A 253 ASP ASP ARG VAL THR ILE LYS LEU LYS ASP ILE TYR GLU SEQRES 13 A 253 GLY ILE GLU GLU GLU ASN VAL ASP HIS VAL ILE LEU ASP SEQRES 14 A 253 LEU PRO GLN PRO GLU ARG VAL VAL GLU HIS ALA ALA LYS SEQRES 15 A 253 ALA LEU LYS PRO GLY GLY PHE PHE VAL ALA TYR THR PRO SEQRES 16 A 253 CYS SER ASN GLN VAL MET ARG LEU HIS GLU LYS LEU ARG SEQRES 17 A 253 GLU PHE LYS ASP TYR PHE MET LYS PRO ARG THR ILE ASN SEQRES 18 A 253 VAL LEU VAL PHE ASP GLN GLU VAL LYS LYS GLU CYS MET SEQRES 19 A 253 ARG PRO ARG THR THR ALA LEU VAL HIS THR GLY TYR ILE SEQRES 20 A 253 THR PHE ALA ARG ARG ILE SEQRES 1 B 253 MET ILE ARG GLU GLY ASP LYS VAL VAL LEU VAL ASP PRO SEQRES 2 B 253 ARG GLY LYS ARG TYR LEU ILE THR VAL SER LYS ARG ASP SEQRES 3 B 253 PHE HIS THR ASP LEU GLY ILE LEU LYS LEU GLU GLU ILE SEQRES 4 B 253 ILE GLY ARG ASN PHE GLY GLU ALA ILE LYS SER HIS LYS SEQRES 5 B 253 GLY HIS GLU PHE LYS ILE LEU ARG PRO ARG ILE VAL ASP SEQRES 6 B 253 TYR LEU ASP LYS MET LYS ARG GLY PRO GLN ILE VAL HIS SEQRES 7 B 253 PRO LYS ASP ALA ALA LEU ILE VAL ALA TYR ALA GLY ILE SEQRES 8 B 253 SER PRO GLY ASP PHE ILE VAL GLU ALA GLY VAL GLY SER SEQRES 9 B 253 GLY ALA LEU THR LEU PHE LEU ALA ASN ILE VAL GLY PRO SEQRES 10 B 253 GLU GLY ARG VAL VAL SER TYR GLU ILE ARG GLU ASP PHE SEQRES 11 B 253 ALA LYS LEU ALA TRP GLU ASN ILE LYS TRP ALA GLY PHE SEQRES 12 B 253 ASP ASP ARG VAL THR ILE LYS LEU LYS ASP ILE TYR GLU SEQRES 13 B 253 GLY ILE GLU GLU GLU ASN VAL ASP HIS VAL ILE LEU ASP SEQRES 14 B 253 LEU PRO GLN PRO GLU ARG VAL VAL GLU HIS ALA ALA LYS SEQRES 15 B 253 ALA LEU LYS PRO GLY GLY PHE PHE VAL ALA TYR THR PRO SEQRES 16 B 253 CYS SER ASN GLN VAL MET ARG LEU HIS GLU LYS LEU ARG SEQRES 17 B 253 GLU PHE LYS ASP TYR PHE MET LYS PRO ARG THR ILE ASN SEQRES 18 B 253 VAL LEU VAL PHE ASP GLN GLU VAL LYS LYS GLU CYS MET SEQRES 19 B 253 ARG PRO ARG THR THR ALA LEU VAL HIS THR GLY TYR ILE SEQRES 20 B 253 THR PHE ALA ARG ARG ILE SEQRES 1 D 253 MET ILE ARG GLU GLY ASP LYS VAL VAL LEU VAL ASP PRO SEQRES 2 D 253 ARG GLY LYS ARG TYR LEU ILE THR VAL SER LYS ARG ASP SEQRES 3 D 253 PHE HIS THR ASP LEU GLY ILE LEU LYS LEU GLU GLU ILE SEQRES 4 D 253 ILE GLY ARG ASN PHE GLY GLU ALA ILE LYS SER HIS LYS SEQRES 5 D 253 GLY HIS GLU PHE LYS ILE LEU ARG PRO ARG ILE VAL ASP SEQRES 6 D 253 TYR LEU ASP LYS MET LYS ARG GLY PRO GLN ILE VAL HIS SEQRES 7 D 253 PRO LYS ASP ALA ALA LEU ILE VAL ALA TYR ALA GLY ILE SEQRES 8 D 253 SER PRO GLY ASP PHE ILE VAL GLU ALA GLY VAL GLY SER SEQRES 9 D 253 GLY ALA LEU THR LEU PHE LEU ALA ASN ILE VAL GLY PRO SEQRES 10 D 253 GLU GLY ARG VAL VAL SER TYR GLU ILE ARG GLU ASP PHE SEQRES 11 D 253 ALA LYS LEU ALA TRP GLU ASN ILE LYS TRP ALA GLY PHE SEQRES 12 D 253 ASP ASP ARG VAL THR ILE LYS LEU LYS ASP ILE TYR GLU SEQRES 13 D 253 GLY ILE GLU GLU GLU ASN VAL ASP HIS VAL ILE LEU ASP SEQRES 14 D 253 LEU PRO GLN PRO GLU ARG VAL VAL GLU HIS ALA ALA LYS SEQRES 15 D 253 ALA LEU LYS PRO GLY GLY PHE PHE VAL ALA TYR THR PRO SEQRES 16 D 253 CYS SER ASN GLN VAL MET ARG LEU HIS GLU LYS LEU ARG SEQRES 17 D 253 GLU PHE LYS ASP TYR PHE MET LYS PRO ARG THR ILE ASN SEQRES 18 D 253 VAL LEU VAL PHE ASP GLN GLU VAL LYS LYS GLU CYS MET SEQRES 19 D 253 ARG PRO ARG THR THR ALA LEU VAL HIS THR GLY TYR ILE SEQRES 20 D 253 THR PHE ALA ARG ARG ILE HET SAH C 301 26 HET SAH A 301 26 HET SAH B 301 26 HET SAH D 301 26 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 5 SAH 4(C14 H20 N6 O5 S) FORMUL 9 HOH *131(H2 O) HELIX 1 1 GLU C 37 ILE C 40 5 4 HELIX 2 2 ARG C 62 MET C 70 1 9 HELIX 3 3 HIS C 78 GLY C 90 1 13 HELIX 4 4 GLY C 105 GLY C 116 1 12 HELIX 5 5 ARG C 127 ALA C 141 1 15 HELIX 6 6 GLY C 142 ASP C 145 5 4 HELIX 7 7 ASP C 153 GLY C 157 5 5 HELIX 8 8 GLN C 172 ARG C 175 5 4 HELIX 9 9 VAL C 176 ALA C 183 1 8 HELIX 10 10 CYS C 196 PHE C 210 1 15 HELIX 11 11 ARG A 62 MET A 70 1 9 HELIX 12 12 HIS A 78 GLY A 90 1 13 HELIX 13 13 GLY A 105 GLY A 116 1 12 HELIX 14 14 ARG A 127 ALA A 141 1 15 HELIX 15 15 GLY A 142 ASP A 145 5 4 HELIX 16 16 GLN A 172 ARG A 175 5 4 HELIX 17 17 VAL A 176 ALA A 183 1 8 HELIX 18 18 CYS A 196 PHE A 210 1 15 HELIX 19 19 GLU B 37 ILE B 39 5 3 HELIX 20 20 ARG B 62 LYS B 69 1 8 HELIX 21 21 HIS B 78 GLY B 90 1 13 HELIX 22 22 GLY B 105 GLY B 116 1 12 HELIX 23 23 ARG B 127 ALA B 141 1 15 HELIX 24 24 ASP B 153 GLY B 157 5 5 HELIX 25 25 GLN B 172 ARG B 175 5 4 HELIX 26 26 VAL B 176 ALA B 183 1 8 HELIX 27 27 CYS B 196 PHE B 210 1 15 HELIX 28 28 GLU D 37 ILE D 40 5 4 HELIX 29 29 ARG D 62 MET D 70 1 9 HELIX 30 30 HIS D 78 GLY D 90 1 13 HELIX 31 31 GLY D 105 GLY D 116 1 12 HELIX 32 32 ARG D 127 GLY D 142 1 16 HELIX 33 33 ASP D 153 GLY D 157 5 5 HELIX 34 34 GLN D 172 ARG D 175 5 4 HELIX 35 35 VAL D 176 ALA D 183 1 8 HELIX 36 36 CYS D 196 PHE D 210 1 15 HELIX 37 37 LYS D 211 PHE D 214 5 4 SHEET 1 A 4 ARG C 17 THR C 21 0 SHEET 2 A 4 LYS C 7 VAL C 11 -1 N VAL C 8 O ILE C 20 SHEET 3 A 4 GLU C 55 LEU C 59 -1 O LEU C 59 N VAL C 9 SHEET 4 A 4 ALA C 47 LYS C 49 -1 N ILE C 48 O PHE C 56 SHEET 1 B 2 ASP C 26 THR C 29 0 SHEET 2 B 2 GLY C 32 LYS C 35 -1 O LEU C 34 N PHE C 27 SHEET 1 C14 VAL C 147 LEU C 151 0 SHEET 2 C14 ARG C 120 GLU C 125 1 N SER C 123 O LYS C 150 SHEET 3 C14 PHE C 96 ALA C 100 1 N ILE C 97 O ARG C 120 SHEET 4 C14 VAL C 163 LEU C 168 1 O ASP C 164 N PHE C 96 SHEET 5 C14 LEU C 184 THR C 194 1 O LYS C 185 N VAL C 163 SHEET 6 C14 TYR C 246 ARG C 251 -1 O TYR C 246 N THR C 194 SHEET 7 C14 ARG C 218 GLU C 228 -1 N ILE C 220 O ILE C 247 SHEET 8 C14 ARG D 218 VAL D 229 -1 O ASN D 221 N PHE C 225 SHEET 9 C14 TYR D 246 ARG D 251 -1 O PHE D 249 N ARG D 218 SHEET 10 C14 LEU D 184 THR D 194 -1 N PHE D 190 O ALA D 250 SHEET 11 C14 VAL D 163 LEU D 168 1 N VAL D 166 O VAL D 191 SHEET 12 C14 PHE D 96 ALA D 100 1 N VAL D 98 O ILE D 167 SHEET 13 C14 ARG D 120 TYR D 124 1 O ARG D 120 N ILE D 97 SHEET 14 C14 VAL D 147 LYS D 150 1 O LYS D 150 N SER D 123 SHEET 1 D 4 ARG C 235 PRO C 236 0 SHEET 2 D 4 ARG C 218 GLU C 228 -1 N GLU C 228 O ARG C 235 SHEET 3 D 4 ARG D 218 VAL D 229 -1 O ASN D 221 N PHE C 225 SHEET 4 D 4 MET D 234 PRO D 236 -1 O ARG D 235 N GLU D 228 SHEET 1 E 2 THR C 239 LEU C 241 0 SHEET 2 E 2 THR A 239 LEU A 241 -1 O ALA A 240 N ALA C 240 SHEET 1 F 4 ARG A 17 THR A 21 0 SHEET 2 F 4 LYS A 7 VAL A 11 -1 N VAL A 8 O ILE A 20 SHEET 3 F 4 GLU A 55 LEU A 59 -1 O LYS A 57 N VAL A 11 SHEET 4 F 4 ALA A 47 LYS A 49 -1 N ILE A 48 O PHE A 56 SHEET 1 G14 VAL A 147 LEU A 151 0 SHEET 2 G14 ARG A 120 GLU A 125 1 N SER A 123 O LYS A 150 SHEET 3 G14 PHE A 96 ALA A 100 1 N ILE A 97 O ARG A 120 SHEET 4 G14 VAL A 163 LEU A 168 1 O ILE A 167 N VAL A 98 SHEET 5 G14 LEU A 184 THR A 194 1 O VAL A 191 N VAL A 166 SHEET 6 G14 TYR A 246 ARG A 251 -1 O TYR A 246 N THR A 194 SHEET 7 G14 ARG A 218 LYS A 230 -1 N ILE A 220 O ILE A 247 SHEET 8 G14 ARG B 218 VAL B 229 -1 O THR B 219 N GLN A 227 SHEET 9 G14 TYR B 246 ARG B 251 -1 O ILE B 247 N ILE B 220 SHEET 10 G14 LEU B 184 THR B 194 -1 N PHE B 190 O ALA B 250 SHEET 11 G14 VAL B 163 LEU B 168 1 N LEU B 168 O VAL B 191 SHEET 12 G14 PHE B 96 ALA B 100 1 N VAL B 98 O HIS B 165 SHEET 13 G14 ARG B 120 GLU B 125 1 O ARG B 120 N ILE B 97 SHEET 14 G14 VAL B 147 LEU B 151 1 O THR B 148 N SER B 123 SHEET 1 H 4 CYS A 233 PRO A 236 0 SHEET 2 H 4 ARG A 218 LYS A 230 -1 N GLU A 228 O ARG A 235 SHEET 3 H 4 ARG B 218 VAL B 229 -1 O THR B 219 N GLN A 227 SHEET 4 H 4 MET B 234 PRO B 236 -1 O ARG B 235 N GLU B 228 SHEET 1 I 4 ARG B 17 THR B 21 0 SHEET 2 I 4 LYS B 7 VAL B 11 -1 N VAL B 8 O ILE B 20 SHEET 3 I 4 GLU B 55 LEU B 59 -1 O LEU B 59 N VAL B 9 SHEET 4 I 4 ALA B 47 LYS B 49 -1 N ILE B 48 O PHE B 56 SHEET 1 J 2 ASP B 26 PHE B 27 0 SHEET 2 J 2 LEU B 34 LYS B 35 -1 O LEU B 34 N PHE B 27 SHEET 1 K 2 THR B 239 LEU B 241 0 SHEET 2 K 2 THR D 239 LEU D 241 -1 O ALA D 240 N ALA B 240 SHEET 1 L 4 ARG D 17 THR D 21 0 SHEET 2 L 4 LYS D 7 VAL D 11 -1 N VAL D 8 O ILE D 20 SHEET 3 L 4 GLU D 55 LEU D 59 -1 O LEU D 59 N VAL D 9 SHEET 4 L 4 ALA D 47 LYS D 49 -1 N ILE D 48 O PHE D 56 SHEET 1 M 2 ASP D 26 THR D 29 0 SHEET 2 M 2 GLY D 32 LYS D 35 -1 O LEU D 34 N PHE D 27 SSBOND 1 CYS C 196 CYS A 233 1555 1555 2.06 SSBOND 2 CYS C 233 CYS A 196 1555 1555 2.04 SSBOND 3 CYS B 196 CYS D 233 1555 1555 2.06 SSBOND 4 CYS B 233 CYS D 196 1555 1555 2.05 CISPEP 1 PRO C 74 GLN C 75 0 0.13 CISPEP 2 PRO B 74 GLN B 75 0 7.89 SITE 1 AC1 11 GLY C 101 GLY C 103 GLU C 125 ILE C 126 SITE 2 AC1 11 PHE C 130 LYS C 152 ASP C 153 ILE C 154 SITE 3 AC1 11 TYR C 155 PRO C 195 HOH C 276 SITE 1 AC2 10 GLY A 101 GLY A 103 GLU A 125 ILE A 126 SITE 2 AC2 10 PHE A 130 ASP A 153 ILE A 154 TYR A 155 SITE 3 AC2 10 ASP A 169 PRO A 171 SITE 1 AC3 13 GLY B 101 GLY B 103 GLU B 125 ILE B 126 SITE 2 AC3 13 PHE B 130 LYS B 152 ASP B 153 ILE B 154 SITE 3 AC3 13 TYR B 155 ASP B 169 LEU B 170 HOH B 271 SITE 4 AC3 13 HOH B 277 SITE 1 AC4 14 GLY D 101 GLY D 103 GLU D 125 ILE D 126 SITE 2 AC4 14 ARG D 127 PHE D 130 ASP D 153 ILE D 154 SITE 3 AC4 14 TYR D 155 ASP D 169 LEU D 170 PRO D 171 SITE 4 AC4 14 PRO D 195 GLN D 199 CRYST1 66.030 127.577 151.396 90.00 90.00 90.00 P 21 21 21 16 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 0.015145 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007838 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006605 0.00000