HEADER TRANSFERASE 25-DEC-06 2E5W TITLE CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM PYROCOCCUS HORIKOSHII TITLE 2 OT3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE SPERMIDINE SYNTHASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: PUTRESCINE AMINOPROPYLTRANSFERASE, SPDSY; COMPND 5 EC: 2.5.1.16; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: OT3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS SPERMIDINE SYNTHASE, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON KEYWDS 2 PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.MIZUTANI,N.KUNISHIMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 3 13-JUL-11 2E5W 1 VERSN REVDAT 2 24-FEB-09 2E5W 1 VERSN REVDAT 1 26-JUN-07 2E5W 0 JRNL AUTH H.MIZUTANI,N.KUNISHIMA JRNL TITL CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM PYROCOCCUS JRNL TITL 2 HORIKOSHII OT3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3506335.740 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 108624 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) : 0.194 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5449 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 16377 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 834 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.011 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8862 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 82 REMARK 3 SOLVENT ATOMS : 827 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 15.93000 REMARK 3 B22 (A**2) : -6.70000 REMARK 3 B33 (A**2) : -9.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 5.88000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.31 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.32 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.78 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) : 1.260 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.980 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.110 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.200 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 54.46 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : MTA.PARAM REMARK 3 PARAMETER FILE 4 : AG3.PARAM REMARK 3 PARAMETER FILE 5 : ACT.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : MTA.TOP REMARK 3 TOPOLOGY FILE 4 : AG3.TOP REMARK 3 TOPOLOGY FILE 5 : ACT.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2E5W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JAN-07. REMARK 100 THE RCSB ID CODE IS RCSB026264. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : BENDING MAGNET REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 108624 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.41300 REMARK 200 R SYM FOR SHELL (I) : 0.34200 REMARK 200 FOR SHELL : 2.290 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1MJF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30%(V/V) PEG 200, 0.1M ACETATE BUFFER, REMARK 280 0.1M NACL, PH 4.5, MICROBATCH, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 74.70550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 61.36750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 74.70550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 61.36750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER. REMARK 300 IN THE ASYMMETRIC UNIT THERE ARE TWO DIMER: CHAIN A + B, AND C + D. 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: 5260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20140 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 350 REMARK 350 BIOMOLECULE: 2 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: 5330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 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 B1176 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 MET B 1 REMARK 465 ARG B 2 REMARK 465 ASP B 3 REMARK 465 THR B 163 REMARK 465 ASP B 164 REMARK 465 PRO B 165 REMARK 465 VAL B 166 REMARK 465 GLY B 167 REMARK 465 PRO B 168 REMARK 465 ALA B 169 REMARK 465 GLU B 170 REMARK 465 MET D 1 REMARK 465 ARG D 2 REMARK 465 ASP D 3 REMARK 465 THR D 163 REMARK 465 ASP D 164 REMARK 465 PRO D 165 REMARK 465 VAL D 166 REMARK 465 GLY D 167 REMARK 465 PRO D 168 REMARK 465 ALA D 169 REMARK 465 GLU D 170 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 ARG A 12 -1.99 80.24 REMARK 500 ARG A 22 165.15 176.59 REMARK 500 ASN A 76 81.11 -162.90 REMARK 500 VAL A 166 -57.32 -124.43 REMARK 500 GLU B 57 79.46 -103.28 REMARK 500 ASN B 76 80.01 -162.83 REMARK 500 SER B 242 38.22 -85.84 REMARK 500 ASN C 76 81.04 -165.44 REMARK 500 ASP C 161 67.17 -116.13 REMARK 500 SER C 162 -167.47 -102.61 REMARK 500 ASN D 76 82.08 -161.94 REMARK 500 ILE D 120 -63.49 -98.08 REMARK 500 TYR D 260 -67.45 -121.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1226 DISTANCE = 5.46 ANGSTROMS REMARK 525 HOH A1259 DISTANCE = 5.61 ANGSTROMS REMARK 525 HOH B1248 DISTANCE = 5.25 ANGSTROMS REMARK 525 HOH B1278 DISTANCE = 5.25 ANGSTROMS REMARK 525 HOH B1286 DISTANCE = 5.38 ANGSTROMS REMARK 525 HOH B1303 DISTANCE = 5.08 ANGSTROMS REMARK 525 HOH B1319 DISTANCE = 5.45 ANGSTROMS REMARK 525 HOH C1218 DISTANCE = 5.79 ANGSTROMS REMARK 525 HOH C1229 DISTANCE = 5.54 ANGSTROMS REMARK 525 HOH C1293 DISTANCE = 5.13 ANGSTROMS REMARK 525 HOH D1167 DISTANCE = 5.34 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT D 1103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 1104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AG3 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AG3 C 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTA A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTA C 1004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: PHO001000211.1 RELATED DB: TARGETDB DBREF 2E5W A 1 280 UNP O57950 SPEE_PYRHO 1 280 DBREF 2E5W B 1 280 UNP O57950 SPEE_PYRHO 1 280 DBREF 2E5W C 1 280 UNP O57950 SPEE_PYRHO 1 280 DBREF 2E5W D 1 280 UNP O57950 SPEE_PYRHO 1 280 SEQRES 1 A 280 MET ARG ASP MET GLU PHE ILE GLU TRP TYR PRO ARG GLY SEQRES 2 A 280 TYR GLY VAL ALA PHE LYS VAL LYS ARG LYS ILE LEU GLU SEQRES 3 A 280 GLU GLN SER GLU TYR GLN LYS ILE GLU VAL TYR GLU THR SEQRES 4 A 280 GLU GLY PHE GLY LYS LEU LEU ALA ILE ASP GLY THR VAL SEQRES 5 A 280 GLN LEU VAL THR GLU GLY GLU LYS SER TYR HIS GLU PRO SEQRES 6 A 280 LEU VAL HIS PRO ALA MET LEU ALA HIS PRO ASN PRO ARG SEQRES 7 A 280 ARG VAL LEU ILE ILE GLY GLY GLY ASP GLY GLY ALA ILE SEQRES 8 A 280 ARG GLU VAL LEU LYS HIS GLU GLU VAL GLU GLU VAL ILE SEQRES 9 A 280 MET VAL GLU ILE ASP LYS LYS VAL ILE GLU ILE SER ALA SEQRES 10 A 280 LYS TYR ILE GLY ILE ASP GLY GLY ILE LEU GLU LYS MET SEQRES 11 A 280 LEU SER ASP LYS HIS GLU LYS GLY LYS LEU ILE ILE GLY SEQRES 12 A 280 ASP GLY VAL LYS PHE ILE GLU GLU ASN SER GLY PHE ASP SEQRES 13 A 280 VAL ILE ILE VAL ASP SER THR ASP PRO VAL GLY PRO ALA SEQRES 14 A 280 GLU MET LEU PHE SER GLU GLU PHE TYR LYS ASN ALA TYR SEQRES 15 A 280 ARG ALA LEU ASN ASP PRO GLY ILE TYR VAL THR GLN ALA SEQRES 16 A 280 GLY SER VAL TYR LEU PHE THR ASP GLU PHE LEU THR ALA SEQRES 17 A 280 TYR ARG LYS MET ARG LYS VAL PHE ASP LYS VAL TYR TYR SEQRES 18 A 280 TYR SER PHE PRO VAL ILE GLY TYR ALA SER PRO TRP ALA SEQRES 19 A 280 PHE LEU VAL GLY VAL LYS GLY SER ILE ASP PHE MET LYS SEQRES 20 A 280 VAL ASP ALA GLU LYS GLY LYS LYS LEU GLY LEU GLU TYR SEQRES 21 A 280 TYR ASP PRO ASP LYS HIS GLU THR LEU PHE GLN MET PRO SEQRES 22 A 280 ARG TYR ILE VAL GLN MET LEU SEQRES 1 B 280 MET ARG ASP MET GLU PHE ILE GLU TRP TYR PRO ARG GLY SEQRES 2 B 280 TYR GLY VAL ALA PHE LYS VAL LYS ARG LYS ILE LEU GLU SEQRES 3 B 280 GLU GLN SER GLU TYR GLN LYS ILE GLU VAL TYR GLU THR SEQRES 4 B 280 GLU GLY PHE GLY LYS LEU LEU ALA ILE ASP GLY THR VAL SEQRES 5 B 280 GLN LEU VAL THR GLU GLY GLU LYS SER TYR HIS GLU PRO SEQRES 6 B 280 LEU VAL HIS PRO ALA MET LEU ALA HIS PRO ASN PRO ARG SEQRES 7 B 280 ARG VAL LEU ILE ILE GLY GLY GLY ASP GLY GLY ALA ILE SEQRES 8 B 280 ARG GLU VAL LEU LYS HIS GLU GLU VAL GLU GLU VAL ILE SEQRES 9 B 280 MET VAL GLU ILE ASP LYS LYS VAL ILE GLU ILE SER ALA SEQRES 10 B 280 LYS TYR ILE GLY ILE ASP GLY GLY ILE LEU GLU LYS MET SEQRES 11 B 280 LEU SER ASP LYS HIS GLU LYS GLY LYS LEU ILE ILE GLY SEQRES 12 B 280 ASP GLY VAL LYS PHE ILE GLU GLU ASN SER GLY PHE ASP SEQRES 13 B 280 VAL ILE ILE VAL ASP SER THR ASP PRO VAL GLY PRO ALA SEQRES 14 B 280 GLU MET LEU PHE SER GLU GLU PHE TYR LYS ASN ALA TYR SEQRES 15 B 280 ARG ALA LEU ASN ASP PRO GLY ILE TYR VAL THR GLN ALA SEQRES 16 B 280 GLY SER VAL TYR LEU PHE THR ASP GLU PHE LEU THR ALA SEQRES 17 B 280 TYR ARG LYS MET ARG LYS VAL PHE ASP LYS VAL TYR TYR SEQRES 18 B 280 TYR SER PHE PRO VAL ILE GLY TYR ALA SER PRO TRP ALA SEQRES 19 B 280 PHE LEU VAL GLY VAL LYS GLY SER ILE ASP PHE MET LYS SEQRES 20 B 280 VAL ASP ALA GLU LYS GLY LYS LYS LEU GLY LEU GLU TYR SEQRES 21 B 280 TYR ASP PRO ASP LYS HIS GLU THR LEU PHE GLN MET PRO SEQRES 22 B 280 ARG TYR ILE VAL GLN MET LEU SEQRES 1 C 280 MET ARG ASP MET GLU PHE ILE GLU TRP TYR PRO ARG GLY SEQRES 2 C 280 TYR GLY VAL ALA PHE LYS VAL LYS ARG LYS ILE LEU GLU SEQRES 3 C 280 GLU GLN SER GLU TYR GLN LYS ILE GLU VAL TYR GLU THR SEQRES 4 C 280 GLU GLY PHE GLY LYS LEU LEU ALA ILE ASP GLY THR VAL SEQRES 5 C 280 GLN LEU VAL THR GLU GLY GLU LYS SER TYR HIS GLU PRO SEQRES 6 C 280 LEU VAL HIS PRO ALA MET LEU ALA HIS PRO ASN PRO ARG SEQRES 7 C 280 ARG VAL LEU ILE ILE GLY GLY GLY ASP GLY GLY ALA ILE SEQRES 8 C 280 ARG GLU VAL LEU LYS HIS GLU GLU VAL GLU GLU VAL ILE SEQRES 9 C 280 MET VAL GLU ILE ASP LYS LYS VAL ILE GLU ILE SER ALA SEQRES 10 C 280 LYS TYR ILE GLY ILE ASP GLY GLY ILE LEU GLU LYS MET SEQRES 11 C 280 LEU SER ASP LYS HIS GLU LYS GLY LYS LEU ILE ILE GLY SEQRES 12 C 280 ASP GLY VAL LYS PHE ILE GLU GLU ASN SER GLY PHE ASP SEQRES 13 C 280 VAL ILE ILE VAL ASP SER THR ASP PRO VAL GLY PRO ALA SEQRES 14 C 280 GLU MET LEU PHE SER GLU GLU PHE TYR LYS ASN ALA TYR SEQRES 15 C 280 ARG ALA LEU ASN ASP PRO GLY ILE TYR VAL THR GLN ALA SEQRES 16 C 280 GLY SER VAL TYR LEU PHE THR ASP GLU PHE LEU THR ALA SEQRES 17 C 280 TYR ARG LYS MET ARG LYS VAL PHE ASP LYS VAL TYR TYR SEQRES 18 C 280 TYR SER PHE PRO VAL ILE GLY TYR ALA SER PRO TRP ALA SEQRES 19 C 280 PHE LEU VAL GLY VAL LYS GLY SER ILE ASP PHE MET LYS SEQRES 20 C 280 VAL ASP ALA GLU LYS GLY LYS LYS LEU GLY LEU GLU TYR SEQRES 21 C 280 TYR ASP PRO ASP LYS HIS GLU THR LEU PHE GLN MET PRO SEQRES 22 C 280 ARG TYR ILE VAL GLN MET LEU SEQRES 1 D 280 MET ARG ASP MET GLU PHE ILE GLU TRP TYR PRO ARG GLY SEQRES 2 D 280 TYR GLY VAL ALA PHE LYS VAL LYS ARG LYS ILE LEU GLU SEQRES 3 D 280 GLU GLN SER GLU TYR GLN LYS ILE GLU VAL TYR GLU THR SEQRES 4 D 280 GLU GLY PHE GLY LYS LEU LEU ALA ILE ASP GLY THR VAL SEQRES 5 D 280 GLN LEU VAL THR GLU GLY GLU LYS SER TYR HIS GLU PRO SEQRES 6 D 280 LEU VAL HIS PRO ALA MET LEU ALA HIS PRO ASN PRO ARG SEQRES 7 D 280 ARG VAL LEU ILE ILE GLY GLY GLY ASP GLY GLY ALA ILE SEQRES 8 D 280 ARG GLU VAL LEU LYS HIS GLU GLU VAL GLU GLU VAL ILE SEQRES 9 D 280 MET VAL GLU ILE ASP LYS LYS VAL ILE GLU ILE SER ALA SEQRES 10 D 280 LYS TYR ILE GLY ILE ASP GLY GLY ILE LEU GLU LYS MET SEQRES 11 D 280 LEU SER ASP LYS HIS GLU LYS GLY LYS LEU ILE ILE GLY SEQRES 12 D 280 ASP GLY VAL LYS PHE ILE GLU GLU ASN SER GLY PHE ASP SEQRES 13 D 280 VAL ILE ILE VAL ASP SER THR ASP PRO VAL GLY PRO ALA SEQRES 14 D 280 GLU MET LEU PHE SER GLU GLU PHE TYR LYS ASN ALA TYR SEQRES 15 D 280 ARG ALA LEU ASN ASP PRO GLY ILE TYR VAL THR GLN ALA SEQRES 16 D 280 GLY SER VAL TYR LEU PHE THR ASP GLU PHE LEU THR ALA SEQRES 17 D 280 TYR ARG LYS MET ARG LYS VAL PHE ASP LYS VAL TYR TYR SEQRES 18 D 280 TYR SER PHE PRO VAL ILE GLY TYR ALA SER PRO TRP ALA SEQRES 19 D 280 PHE LEU VAL GLY VAL LYS GLY SER ILE ASP PHE MET LYS SEQRES 20 D 280 VAL ASP ALA GLU LYS GLY LYS LYS LEU GLY LEU GLU TYR SEQRES 21 D 280 TYR ASP PRO ASP LYS HIS GLU THR LEU PHE GLN MET PRO SEQRES 22 D 280 ARG TYR ILE VAL GLN MET LEU HET ACT B1101 4 HET ACT A1102 4 HET ACT D1103 4 HET ACT C1104 4 HET AG3 A1001 13 HET AG3 C1002 13 HET MTA A1003 20 HET MTA C1004 20 HETNAM ACT ACETATE ION HETNAM AG3 1-{4-[(3-AMINOPROPYL)AMINO]BUTYL}GUANIDINE HETNAM MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE HETSYN AG3 N1-AMINOPROPYLAGMATINE FORMUL 5 ACT 4(C2 H3 O2 1-) FORMUL 9 AG3 2(C8 H21 N5) FORMUL 11 MTA 2(C11 H15 N5 O3 S) FORMUL 13 HOH *827(H2 O) HELIX 1 1 GLU A 59 HIS A 74 1 16 HELIX 2 2 GLY A 88 LEU A 95 1 8 HELIX 3 3 ASP A 109 ILE A 120 1 12 HELIX 4 4 GLY A 125 SER A 132 1 8 HELIX 5 5 ASP A 144 GLU A 150 1 7 HELIX 6 6 ALA A 169 PHE A 173 5 5 HELIX 7 7 SER A 174 ALA A 184 1 11 HELIX 8 8 PHE A 201 LYS A 214 1 14 HELIX 9 9 ASP A 249 LYS A 255 1 7 HELIX 10 10 ASP A 262 GLN A 271 5 10 HELIX 11 11 PRO A 273 GLN A 278 1 6 HELIX 12 12 GLU B 59 HIS B 74 1 16 HELIX 13 13 GLY B 88 LEU B 95 1 8 HELIX 14 14 ASP B 109 ILE B 120 1 12 HELIX 15 15 GLY B 125 SER B 132 1 8 HELIX 16 16 ASP B 144 ASN B 152 1 9 HELIX 17 17 SER B 174 ALA B 184 1 11 HELIX 18 18 PHE B 201 LYS B 214 1 14 HELIX 19 19 ASP B 249 LYS B 255 1 7 HELIX 20 20 ASP B 262 GLN B 271 5 10 HELIX 21 21 PRO B 273 GLN B 278 1 6 HELIX 22 22 GLU C 59 HIS C 74 1 16 HELIX 23 23 GLY C 88 LEU C 95 1 8 HELIX 24 24 ASP C 109 ILE C 120 1 12 HELIX 25 25 GLY C 125 SER C 132 1 8 HELIX 26 26 ASP C 144 ASN C 152 1 9 HELIX 27 27 ALA C 169 PHE C 173 5 5 HELIX 28 28 SER C 174 ALA C 184 1 11 HELIX 29 29 PHE C 201 LYS C 214 1 14 HELIX 30 30 ASP C 249 LYS C 255 1 7 HELIX 31 31 ASP C 262 GLN C 271 5 10 HELIX 32 32 PRO C 273 GLN C 278 1 6 HELIX 33 33 GLU D 59 HIS D 74 1 16 HELIX 34 34 GLY D 88 LEU D 95 1 8 HELIX 35 35 ASP D 109 ILE D 120 1 12 HELIX 36 36 GLY D 125 SER D 132 1 8 HELIX 37 37 ASP D 144 ASN D 152 1 9 HELIX 38 38 SER D 174 ALA D 184 1 11 HELIX 39 39 PHE D 201 LYS D 214 1 14 HELIX 40 40 ASP D 249 LYS D 255 1 7 HELIX 41 41 ASP D 262 GLN D 271 5 10 HELIX 42 42 PRO D 273 LEU D 280 1 8 SHEET 1 A 4 MET A 4 TYR A 10 0 SHEET 2 A 4 TYR A 14 GLN A 28 -1 O TYR A 14 N TYR A 10 SHEET 3 A 4 TYR B 14 GLN B 28 -1 O ALA B 17 N GLY A 15 SHEET 4 A 4 GLU B 5 TYR B 10 -1 N TYR B 10 O TYR B 14 SHEET 1 B 8 THR A 51 VAL A 55 0 SHEET 2 B 8 LYS A 44 ILE A 48 -1 N LEU A 46 O GLN A 53 SHEET 3 B 8 LYS A 33 THR A 39 -1 N GLU A 35 O ALA A 47 SHEET 4 B 8 TYR A 14 GLN A 28 -1 N LYS A 21 O GLU A 38 SHEET 5 B 8 TYR B 14 GLN B 28 -1 O ALA B 17 N GLY A 15 SHEET 6 B 8 LYS B 33 THR B 39 -1 O ILE B 34 N GLU B 27 SHEET 7 B 8 LYS B 44 ILE B 48 -1 O ALA B 47 N GLU B 35 SHEET 8 B 8 THR B 51 VAL B 55 -1 O GLN B 53 N LEU B 46 SHEET 1 C 7 GLY A 138 ILE A 142 0 SHEET 2 C 7 GLU A 102 GLU A 107 1 N MET A 105 O ILE A 141 SHEET 3 C 7 ARG A 79 GLY A 84 1 N ILE A 82 O ILE A 104 SHEET 4 C 7 PHE A 155 ASP A 161 1 O ILE A 159 N LEU A 81 SHEET 5 C 7 LEU A 185 SER A 197 1 O VAL A 192 N VAL A 160 SHEET 6 C 7 TRP A 233 LYS A 240 -1 O ALA A 234 N ALA A 195 SHEET 7 C 7 LYS A 218 PHE A 224 -1 N TYR A 220 O VAL A 237 SHEET 1 D 7 GLY B 138 ILE B 142 0 SHEET 2 D 7 GLU B 102 GLU B 107 1 N MET B 105 O LYS B 139 SHEET 3 D 7 ARG B 79 GLY B 84 1 N GLY B 84 O VAL B 106 SHEET 4 D 7 PHE B 155 ASP B 161 1 O ASP B 161 N ILE B 83 SHEET 5 D 7 LEU B 185 SER B 197 1 O VAL B 192 N ILE B 158 SHEET 6 D 7 TRP B 233 LYS B 240 -1 O ALA B 234 N ALA B 195 SHEET 7 D 7 LYS B 218 PHE B 224 -1 N TYR B 220 O VAL B 237 SHEET 1 E 4 MET C 4 TYR C 10 0 SHEET 2 E 4 TYR C 14 GLN C 28 -1 O TYR C 14 N TYR C 10 SHEET 3 E 4 TYR D 14 GLN D 28 -1 O GLY D 15 N ALA C 17 SHEET 4 E 4 GLU D 5 TYR D 10 -1 N TYR D 10 O TYR D 14 SHEET 1 F 8 THR C 51 VAL C 55 0 SHEET 2 F 8 LYS C 44 ILE C 48 -1 N LEU C 46 O GLN C 53 SHEET 3 F 8 LYS C 33 THR C 39 -1 N GLU C 35 O ALA C 47 SHEET 4 F 8 TYR C 14 GLN C 28 -1 N GLU C 27 O ILE C 34 SHEET 5 F 8 TYR D 14 GLN D 28 -1 O GLY D 15 N ALA C 17 SHEET 6 F 8 LYS D 33 THR D 39 -1 O ILE D 34 N GLU D 27 SHEET 7 F 8 LYS D 44 ILE D 48 -1 O ALA D 47 N GLU D 35 SHEET 8 F 8 THR D 51 VAL D 55 -1 O GLN D 53 N LEU D 46 SHEET 1 G 7 GLY C 138 ILE C 142 0 SHEET 2 G 7 GLU C 102 GLU C 107 1 N MET C 105 O LYS C 139 SHEET 3 G 7 ARG C 79 GLY C 84 1 N ILE C 82 O ILE C 104 SHEET 4 G 7 PHE C 155 ASP C 161 1 O ILE C 159 N LEU C 81 SHEET 5 G 7 LEU C 185 SER C 197 1 O VAL C 192 N VAL C 160 SHEET 6 G 7 TRP C 233 LYS C 240 -1 O ALA C 234 N ALA C 195 SHEET 7 G 7 LYS C 218 PHE C 224 -1 N PHE C 224 O TRP C 233 SHEET 1 H 7 GLY D 138 ILE D 142 0 SHEET 2 H 7 GLU D 102 GLU D 107 1 N MET D 105 O ILE D 141 SHEET 3 H 7 ARG D 79 GLY D 84 1 N ILE D 82 O ILE D 104 SHEET 4 H 7 PHE D 155 ASP D 161 1 O ASP D 161 N ILE D 83 SHEET 5 H 7 LEU D 185 SER D 197 1 O VAL D 192 N ILE D 158 SHEET 6 H 7 TRP D 233 LYS D 240 -1 O ALA D 234 N ALA D 195 SHEET 7 H 7 LYS D 218 PHE D 224 -1 N TYR D 220 O VAL D 237 CISPEP 1 ASP A 187 PRO A 188 0 0.17 CISPEP 2 SER A 231 PRO A 232 0 0.01 CISPEP 3 ASP B 187 PRO B 188 0 0.16 CISPEP 4 SER B 231 PRO B 232 0 0.13 CISPEP 5 ASP C 187 PRO C 188 0 0.28 CISPEP 6 SER C 231 PRO C 232 0 0.03 CISPEP 7 ASP D 187 PRO D 188 0 0.36 CISPEP 8 SER D 231 PRO D 232 0 0.07 SITE 1 AC1 4 HOH A1130 SER B 231 HOH B1115 HOH B1123 SITE 1 AC2 2 SER A 231 HOH A1103 SITE 1 AC3 4 HOH C1119 HOH C1130 SER D 231 HOH D1107 SITE 1 AC4 3 SER C 231 HOH C1107 HOH C1192 SITE 1 AC5 14 GLU A 8 TYR A 10 VAL A 52 GLN A 53 SITE 2 AC5 14 TYR A 62 HIS A 63 ASP A 87 ASP A 161 SITE 3 AC5 14 SER A 162 ASP A 164 GLN A 194 TYR A 229 SITE 4 AC5 14 TRP A 233 MTA A1003 SITE 1 AC6 14 GLU C 8 TYR C 10 VAL C 52 GLN C 53 SITE 2 AC6 14 TYR C 62 HIS C 63 ASP C 87 ASP C 161 SITE 3 AC6 14 SER C 162 ASP C 164 GLN C 194 TYR C 229 SITE 4 AC6 14 TRP C 233 MTA C1004 SITE 1 AC7 22 GLN A 32 ILE A 48 GLN A 53 GLY A 84 SITE 2 AC7 22 GLY A 85 GLY A 86 ASP A 87 VAL A 106 SITE 3 AC7 22 GLU A 107 ILE A 108 ASP A 109 VAL A 112 SITE 4 AC7 22 GLY A 143 ASP A 144 GLY A 145 ASP A 161 SITE 5 AC7 22 SER A 162 THR A 163 PRO A 168 ALA A 169 SITE 6 AC7 22 LEU A 172 AG3 A1001 SITE 1 AC8 20 GLN C 32 ILE C 48 GLN C 53 GLY C 84 SITE 2 AC8 20 GLY C 85 GLY C 86 ASP C 87 VAL C 106 SITE 3 AC8 20 GLU C 107 ILE C 108 ASP C 109 VAL C 112 SITE 4 AC8 20 ASP C 144 GLY C 145 ASP C 161 SER C 162 SITE 5 AC8 20 THR C 163 PRO C 168 ALA C 169 AG3 C1002 CRYST1 149.411 122.735 102.085 90.00 117.69 90.00 C 1 2 1 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 0.006693 0.000000 0.003512 0.00000 SCALE2 0.000000 0.008148 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011063 0.00000 MASTER 363 0 8 42 52 0 23 6 0 0 0 88 END