PDB Short entry for 2CMH HEADER TRANSFERASE 08-MAY-06 2CMH TITLE CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM HELICOBACTER PYLORI COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPERMIDINE SYNTHASE; COMPND 3 CHAIN: A, B, C; 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: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 85962; SOURCE 4 STRAIN: 26695; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: SG13009; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE-30 KEYWDS PUTRESCINE AMINOPROPYLTRANSFERASE, SPERMIDINE BIOSYNTHESIS, SPEE, KEYWDS 2 TRANSFERASE, SPERMIDINE SYNTHASE, HELICOBACTER PYLORI, POLYAMINE KEYWDS 3 BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR Y.-J.SUN,P.-K.LU REVDAT 4 08-MAY-24 2CMH 1 REMARK REVDAT 3 20-NOV-13 2CMH 1 SOURCE REMARK VERSN FORMUL REVDAT 2 24-FEB-09 2CMH 1 VERSN REVDAT 1 08-MAY-07 2CMH 0 JRNL AUTH P.-K.LU,J.-Y.TSAI,H.Y.CHIEN,H.HUANG,C.-H.CHU,Y.-J.SUN JRNL TITL CRYSTAL STRUCTURE OF HELICOBACTER PYLORI SPERMIDINE JRNL TITL 2 SYNTHASE: A ROSSMANN-LIKE FOLD WITH A DISTINCT ACTIVE SITE JRNL REF PROTEINS: STRUCT., FUNCT., V. 67 743 2007 JRNL REF 2 BIOINF. JRNL REFN ISSN 0887-3585 JRNL PMID 17357156 JRNL DOI 10.1002/PROT.21315 REMARK 2 REMARK 2 RESOLUTION. 2.30 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 20549.920 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 38619 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 : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1932 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5717 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 292 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6452 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 461 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.78000 REMARK 3 B22 (A**2) : 0.51000 REMARK 3 B33 (A**2) : -3.28000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.14 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) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.28 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) : 24.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.850 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.44 REMARK 3 BSOL : 88.60 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.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2CMH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1290023165. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL12B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40302 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.90 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 45.8900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.00 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 10.40 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH 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 (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 71.97400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 71.97400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 49.26300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.23400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 49.26300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.23400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 71.97400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 49.26300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 63.23400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 71.97400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 49.26300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 63.23400 REMARK 290 SMTRY3 8 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: THIS PROTEIN WAS DETECTED AS DIMER/TETRAMER REMARK 300 WITH SIZE-EXCLUSION CHROMATOGRAPHY. THE REMARK 300 TETRAMERIC STATES WERE OBSERVED IN 2CMH AS TYPE I REMARK 300 TETRAMER (BCB'C'/BIOMOLECULE 1) AND TYPE II REMARK 300 TETRAMER (BCAA'/BIOMOLECULE 2). 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: 9030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 71.97400 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS 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 126.46800 REMARK 350 BIOMT3 1 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 C2023 LIES ON A SPECIAL POSITION. REMARK 375 HOH C2107 LIES ON A SPECIAL POSITION. REMARK 375 HOH C2121 LIES ON A SPECIAL POSITION. 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 LEU A 21 CG CD1 CD2 REMARK 470 GLU A 27 CG CD OE1 OE2 REMARK 470 PHE A 39 CG CD1 CD2 CE1 CE2 CZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2063 O HOH A 2063 4565 0.92 REMARK 500 O HOH C 2120 O HOH C 2120 3655 0.94 REMARK 500 O HOH C 2122 O HOH C 2122 3655 1.06 REMARK 500 O HOH C 2022 O HOH C 2022 3555 2.18 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 19 167.05 178.96 REMARK 500 PHE A 91 3.59 -63.60 REMARK 500 GLN A 101 119.18 -167.35 REMARK 500 ILE A 204 -43.62 -165.02 REMARK 500 LYS A 216 -34.95 -133.53 REMARK 500 TYR A 236 -50.76 -129.29 REMARK 500 LYS A 257 -86.61 -31.29 REMARK 500 SER B 26 -169.51 -117.68 REMARK 500 ASN B 46 58.85 39.42 REMARK 500 GLN B 101 105.06 -164.66 REMARK 500 LEU B 202 -1.88 71.38 REMARK 500 LYS B 216 -8.11 -170.37 REMARK 500 TYR B 236 -55.56 -127.66 REMARK 500 HIS C 28 -28.06 -153.93 REMARK 500 ILE C 57 -70.51 -56.77 REMARK 500 ILE C 111 -41.44 -26.32 REMARK 500 LEU C 202 -17.55 74.74 REMARK 500 ILE C 204 4.87 -64.52 REMARK 500 LYS C 216 25.13 -160.82 REMARK 500 TYR C 236 -54.22 -126.55 REMARK 500 LYS C 257 -69.83 -27.14 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 A2005 DISTANCE = 9.48 ANGSTROMS REMARK 525 HOH A2006 DISTANCE = 7.89 ANGSTROMS REMARK 525 HOH A2007 DISTANCE = 7.14 ANGSTROMS REMARK 525 HOH A2008 DISTANCE = 8.05 ANGSTROMS REMARK 525 HOH A2009 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A2010 DISTANCE = 7.97 ANGSTROMS REMARK 525 HOH A2011 DISTANCE = 8.93 ANGSTROMS REMARK 525 HOH A2012 DISTANCE = 7.67 ANGSTROMS REMARK 525 HOH A2013 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH A2018 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH A2021 DISTANCE = 8.31 ANGSTROMS REMARK 525 HOH A2022 DISTANCE = 9.14 ANGSTROMS REMARK 525 HOH A2024 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A2027 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A2032 DISTANCE = 8.24 ANGSTROMS REMARK 525 HOH A2038 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A2039 DISTANCE = 9.74 ANGSTROMS REMARK 525 HOH A2040 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A2043 DISTANCE = 9.12 ANGSTROMS REMARK 525 HOH A2047 DISTANCE = 8.35 ANGSTROMS REMARK 525 HOH A2056 DISTANCE = 7.11 ANGSTROMS REMARK 525 HOH A2062 DISTANCE = 10.59 ANGSTROMS REMARK 525 HOH A2069 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A2072 DISTANCE = 6.53 ANGSTROMS REMARK 525 HOH A2073 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A2080 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH A2089 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A2092 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH A2093 DISTANCE = 8.74 ANGSTROMS REMARK 525 HOH A2094 DISTANCE = 7.75 ANGSTROMS REMARK 525 HOH A2101 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH A2105 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A2106 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A2114 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH B2004 DISTANCE = 9.73 ANGSTROMS REMARK 525 HOH B2005 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH B2009 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH B2010 DISTANCE = 7.94 ANGSTROMS REMARK 525 HOH B2015 DISTANCE = 7.80 ANGSTROMS REMARK 525 HOH B2018 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH B2019 DISTANCE = 6.95 ANGSTROMS REMARK 525 HOH B2020 DISTANCE = 6.91 ANGSTROMS REMARK 525 HOH B2035 DISTANCE = 7.28 ANGSTROMS REMARK 525 HOH B2039 DISTANCE = 9.35 ANGSTROMS REMARK 525 HOH B2043 DISTANCE = 7.39 ANGSTROMS REMARK 525 HOH B2047 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH B2058 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH B2060 DISTANCE = 6.92 ANGSTROMS REMARK 525 HOH B2061 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH B2064 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH B2067 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH C2002 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH C2003 DISTANCE = 7.13 ANGSTROMS REMARK 525 HOH C2004 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH C2015 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH C2016 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH C2019 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH C2021 DISTANCE = 7.02 ANGSTROMS REMARK 525 HOH C2024 DISTANCE = 7.02 ANGSTROMS REMARK 525 HOH C2025 DISTANCE = 8.75 ANGSTROMS REMARK 525 HOH C2026 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH C2027 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH C2038 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH C2040 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH C2045 DISTANCE = 9.87 ANGSTROMS REMARK 525 HOH C2046 DISTANCE = 8.41 ANGSTROMS REMARK 525 HOH C2048 DISTANCE = 7.04 ANGSTROMS REMARK 525 HOH C2054 DISTANCE = 7.95 ANGSTROMS REMARK 525 HOH C2058 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH C2077 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH C2078 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH C2079 DISTANCE = 6.21 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CMG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM HELICOBACTER PYLORI DBREF 2CMH A 1 262 UNP O25503 SPEE_HELPY 1 262 DBREF 2CMH B 1 262 UNP O25503 SPEE_HELPY 1 262 DBREF 2CMH C 1 262 UNP O25503 SPEE_HELPY 1 262 SEQRES 1 A 262 MET TRP ILE THR GLN GLU ILE THR PRO TYR LEU ARG LYS SEQRES 2 A 262 GLU TYR THR ILE GLU ALA LYS LEU LEU ASP VAL ARG SER SEQRES 3 A 262 GLU HIS ASN ILE LEU GLU ILE PHE LYS SER LYS ASP PHE SEQRES 4 A 262 GLY GLU ILE ALA MET LEU ASN ARG GLN LEU LEU PHE LYS SEQRES 5 A 262 ASN PHE LEU HIS ILE GLU SER GLU LEU LEU ALA HIS MET SEQRES 6 A 262 GLY GLY CYS THR LYS LYS GLU LEU LYS GLU VAL LEU ILE SEQRES 7 A 262 VAL ASP GLY PHE ASP LEU GLU LEU ALA HIS GLN LEU PHE SEQRES 8 A 262 LYS TYR ASP THR HIS ILE ASP PHE VAL GLN ALA ASP GLU SEQRES 9 A 262 LYS ILE LEU ASP SER PHE ILE SER PHE PHE PRO HIS PHE SEQRES 10 A 262 HIS GLU VAL LYS ASN ASN LYS ASN PHE THR HIS ALA LYS SEQRES 11 A 262 GLN LEU LEU ASP LEU ASP ILE LYS LYS TYR ASP LEU ILE SEQRES 12 A 262 PHE CYS LEU GLN GLU PRO ASP ILE HIS ARG ILE ASP GLY SEQRES 13 A 262 LEU LYS ARG MET LEU LYS GLU ASP GLY VAL PHE ILE SER SEQRES 14 A 262 VAL ALA LYS HIS PRO LEU LEU GLU HIS VAL SER MET GLN SEQRES 15 A 262 ASN ALA LEU LYS ASN MET GLY GLY VAL PHE SER VAL ALA SEQRES 16 A 262 MET PRO PHE VAL ALA PRO LEU ARG ILE LEU SER ASN LYS SEQRES 17 A 262 GLY TYR ILE TYR ALA SER PHE LYS THR HIS PRO LEU LYS SEQRES 18 A 262 ASP LEU MET THR PRO LYS ILE GLU ALA LEU THR SER VAL SEQRES 19 A 262 ARG TYR TYR ASN GLU ASP ILE HIS ARG ALA ALA PHE ALA SEQRES 20 A 262 LEU PRO LYS ASN LEU GLN GLU VAL PHE LYS ASP ASN ILE SEQRES 21 A 262 LYS SER SEQRES 1 B 262 MET TRP ILE THR GLN GLU ILE THR PRO TYR LEU ARG LYS SEQRES 2 B 262 GLU TYR THR ILE GLU ALA LYS LEU LEU ASP VAL ARG SER SEQRES 3 B 262 GLU HIS ASN ILE LEU GLU ILE PHE LYS SER LYS ASP PHE SEQRES 4 B 262 GLY GLU ILE ALA MET LEU ASN ARG GLN LEU LEU PHE LYS SEQRES 5 B 262 ASN PHE LEU HIS ILE GLU SER GLU LEU LEU ALA HIS MET SEQRES 6 B 262 GLY GLY CYS THR LYS LYS GLU LEU LYS GLU VAL LEU ILE SEQRES 7 B 262 VAL ASP GLY PHE ASP LEU GLU LEU ALA HIS GLN LEU PHE SEQRES 8 B 262 LYS TYR ASP THR HIS ILE ASP PHE VAL GLN ALA ASP GLU SEQRES 9 B 262 LYS ILE LEU ASP SER PHE ILE SER PHE PHE PRO HIS PHE SEQRES 10 B 262 HIS GLU VAL LYS ASN ASN LYS ASN PHE THR HIS ALA LYS SEQRES 11 B 262 GLN LEU LEU ASP LEU ASP ILE LYS LYS TYR ASP LEU ILE SEQRES 12 B 262 PHE CYS LEU GLN GLU PRO ASP ILE HIS ARG ILE ASP GLY SEQRES 13 B 262 LEU LYS ARG MET LEU LYS GLU ASP GLY VAL PHE ILE SER SEQRES 14 B 262 VAL ALA LYS HIS PRO LEU LEU GLU HIS VAL SER MET GLN SEQRES 15 B 262 ASN ALA LEU LYS ASN MET GLY GLY VAL PHE SER VAL ALA SEQRES 16 B 262 MET PRO PHE VAL ALA PRO LEU ARG ILE LEU SER ASN LYS SEQRES 17 B 262 GLY TYR ILE TYR ALA SER PHE LYS THR HIS PRO LEU LYS SEQRES 18 B 262 ASP LEU MET THR PRO LYS ILE GLU ALA LEU THR SER VAL SEQRES 19 B 262 ARG TYR TYR ASN GLU ASP ILE HIS ARG ALA ALA PHE ALA SEQRES 20 B 262 LEU PRO LYS ASN LEU GLN GLU VAL PHE LYS ASP ASN ILE SEQRES 21 B 262 LYS SER SEQRES 1 C 262 MET TRP ILE THR GLN GLU ILE THR PRO TYR LEU ARG LYS SEQRES 2 C 262 GLU TYR THR ILE GLU ALA LYS LEU LEU ASP VAL ARG SER SEQRES 3 C 262 GLU HIS ASN ILE LEU GLU ILE PHE LYS SER LYS ASP PHE SEQRES 4 C 262 GLY GLU ILE ALA MET LEU ASN ARG GLN LEU LEU PHE LYS SEQRES 5 C 262 ASN PHE LEU HIS ILE GLU SER GLU LEU LEU ALA HIS MET SEQRES 6 C 262 GLY GLY CYS THR LYS LYS GLU LEU LYS GLU VAL LEU ILE SEQRES 7 C 262 VAL ASP GLY PHE ASP LEU GLU LEU ALA HIS GLN LEU PHE SEQRES 8 C 262 LYS TYR ASP THR HIS ILE ASP PHE VAL GLN ALA ASP GLU SEQRES 9 C 262 LYS ILE LEU ASP SER PHE ILE SER PHE PHE PRO HIS PHE SEQRES 10 C 262 HIS GLU VAL LYS ASN ASN LYS ASN PHE THR HIS ALA LYS SEQRES 11 C 262 GLN LEU LEU ASP LEU ASP ILE LYS LYS TYR ASP LEU ILE SEQRES 12 C 262 PHE CYS LEU GLN GLU PRO ASP ILE HIS ARG ILE ASP GLY SEQRES 13 C 262 LEU LYS ARG MET LEU LYS GLU ASP GLY VAL PHE ILE SER SEQRES 14 C 262 VAL ALA LYS HIS PRO LEU LEU GLU HIS VAL SER MET GLN SEQRES 15 C 262 ASN ALA LEU LYS ASN MET GLY GLY VAL PHE SER VAL ALA SEQRES 16 C 262 MET PRO PHE VAL ALA PRO LEU ARG ILE LEU SER ASN LYS SEQRES 17 C 262 GLY TYR ILE TYR ALA SER PHE LYS THR HIS PRO LEU LYS SEQRES 18 C 262 ASP LEU MET THR PRO LYS ILE GLU ALA LEU THR SER VAL SEQRES 19 C 262 ARG TYR TYR ASN GLU ASP ILE HIS ARG ALA ALA PHE ALA SEQRES 20 C 262 LEU PRO LYS ASN LEU GLN GLU VAL PHE LYS ASP ASN ILE SEQRES 21 C 262 LYS SER FORMUL 4 HOH *461(H2 O) HELIX 1 1 LEU A 55 CYS A 68 1 14 HELIX 2 2 ASP A 83 PHE A 91 1 9 HELIX 3 3 ASP A 103 SER A 109 1 7 HELIX 4 4 HIS A 116 ASN A 122 1 7 HELIX 5 5 GLN A 131 LEU A 135 5 5 HELIX 6 6 ASP A 150 ARG A 159 1 10 HELIX 7 7 HIS A 173 GLY A 190 1 18 HELIX 8 8 MET A 224 GLU A 229 1 6 HELIX 9 9 ASN A 238 PHE A 246 1 9 HELIX 10 10 PRO A 249 LYS A 257 1 9 HELIX 11 11 ASP A 258 ILE A 260 5 3 HELIX 12 12 LEU B 55 CYS B 68 1 14 HELIX 13 13 ASP B 83 PHE B 91 1 9 HELIX 14 14 ASP B 103 SER B 109 1 7 HELIX 15 15 HIS B 116 ASN B 122 1 7 HELIX 16 16 GLN B 131 LEU B 135 5 5 HELIX 17 17 ASP B 150 ARG B 159 1 10 HELIX 18 18 GLU B 177 GLY B 190 1 14 HELIX 19 19 MET B 224 LEU B 231 1 8 HELIX 20 20 ASN B 238 ALA B 245 1 8 HELIX 21 21 PRO B 249 PHE B 256 1 8 HELIX 22 22 PHE C 54 CYS C 68 1 15 HELIX 23 23 ASP C 83 PHE C 91 1 9 HELIX 24 24 ASP C 103 SER C 109 1 7 HELIX 25 25 HIS C 116 ASN C 122 1 7 HELIX 26 26 GLN C 131 LEU C 135 5 5 HELIX 27 27 ASP C 150 ARG C 159 1 10 HELIX 28 28 GLU C 177 GLY C 190 1 14 HELIX 29 29 MET C 224 LEU C 231 1 8 HELIX 30 30 ASN C 238 ALA C 245 1 8 HELIX 31 31 PRO C 249 LYS C 257 1 9 HELIX 32 32 ASP C 258 ILE C 260 5 3 SHEET 1 AA 2 TRP A 2 THR A 8 0 SHEET 2 AA 2 LEU A 11 THR A 16 -1 O LEU A 11 N ILE A 7 SHEET 1 AB 4 ALA A 19 ARG A 25 0 SHEET 2 AB 4 ILE A 30 SER A 36 -1 O LEU A 31 N VAL A 24 SHEET 3 AB 4 GLY A 40 LEU A 45 -1 O GLY A 40 N SER A 36 SHEET 4 AB 4 GLN A 48 PHE A 51 -1 O GLN A 48 N LEU A 45 SHEET 1 AC 7 PHE A 126 ALA A 129 0 SHEET 2 AC 7 HIS A 96 VAL A 100 1 O ILE A 97 N THR A 127 SHEET 3 AC 7 GLU A 75 VAL A 79 1 O VAL A 76 N ASP A 98 SHEET 4 AC 7 TYR A 140 CYS A 145 1 N ASP A 141 O GLU A 75 SHEET 5 AC 7 LEU A 161 LYS A 172 1 N LYS A 162 O TYR A 140 SHEET 6 AC 7 LYS A 208 SER A 214 -1 O GLY A 209 N ALA A 171 SHEET 7 AC 7 VAL A 194 PHE A 198 -1 O VAL A 194 N SER A 214 SHEET 1 BA 4 TRP B 2 THR B 8 0 SHEET 2 BA 4 LEU B 11 THR B 16 -1 O LEU B 11 N THR B 8 SHEET 3 BA 4 LEU C 11 THR C 16 -1 O ARG C 12 N GLU B 14 SHEET 4 BA 4 TRP C 2 THR C 8 -1 O ILE C 3 N TYR C 15 SHEET 1 BB 4 ALA B 19 ARG B 25 0 SHEET 2 BB 4 ILE B 30 LYS B 35 -1 O LEU B 31 N VAL B 24 SHEET 3 BB 4 GLU B 41 LEU B 45 -1 O ILE B 42 N PHE B 34 SHEET 4 BB 4 GLN B 48 PHE B 51 -1 O GLN B 48 N LEU B 45 SHEET 1 BC 7 PHE B 126 ALA B 129 0 SHEET 2 BC 7 HIS B 96 VAL B 100 1 O ILE B 97 N THR B 127 SHEET 3 BC 7 GLU B 75 VAL B 79 1 O VAL B 76 N ASP B 98 SHEET 4 BC 7 TYR B 140 CYS B 145 1 N ASP B 141 O GLU B 75 SHEET 5 BC 7 LEU B 161 ALA B 171 1 N LYS B 162 O TYR B 140 SHEET 6 BC 7 GLY B 209 SER B 214 -1 O GLY B 209 N ALA B 171 SHEET 7 BC 7 VAL B 194 PHE B 198 -1 O VAL B 194 N SER B 214 SHEET 1 CA 4 ALA C 19 ARG C 25 0 SHEET 2 CA 4 ILE C 30 SER C 36 -1 O LEU C 31 N VAL C 24 SHEET 3 CA 4 GLY C 40 LEU C 45 -1 O GLY C 40 N SER C 36 SHEET 4 CA 4 LEU C 49 PHE C 51 -1 O LEU C 50 N ALA C 43 SHEET 1 CB 7 PHE C 126 ALA C 129 0 SHEET 2 CB 7 HIS C 96 VAL C 100 1 O ILE C 97 N THR C 127 SHEET 3 CB 7 GLU C 75 VAL C 79 1 O VAL C 76 N ASP C 98 SHEET 4 CB 7 TYR C 140 CYS C 145 1 N ASP C 141 O GLU C 75 SHEET 5 CB 7 LEU C 161 ALA C 171 1 N LYS C 162 O TYR C 140 SHEET 6 CB 7 GLY C 209 SER C 214 -1 O GLY C 209 N ALA C 171 SHEET 7 CB 7 VAL C 194 PHE C 198 -1 O VAL C 194 N SER C 214 CRYST1 98.526 126.468 143.948 90.00 90.00 90.00 C 2 2 21 24 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 0.010150 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007907 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006947 0.00000