PDB Short entry for 2O07 HEADER TRANSFERASE 27-NOV-06 2O07 TITLE HUMAN SPERMIDINE SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPERMIDINE SYNTHASE; COMPND 3 CHAIN: A, B; 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: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SRM, SPS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SPERMIDINE SYNTHASE, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, SGC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.MIN,H.WU,H.ZENG,P.LOPPNAU,J.WEIGELT,M.SUNDSTROM,C.H.ARROWSMITH, AUTHOR 2 A.M.EDWARDS,A.BOCHKAREV,A.N.PLOTNIKOV,STRUCTURAL GENOMICS CONSORTIUM AUTHOR 3 (SGC) REVDAT 4 27-DEC-23 2O07 1 REMARK SEQADV REVDAT 3 24-FEB-09 2O07 1 VERSN REVDAT 2 18-SEP-07 2O07 1 JRNL REVDAT 1 12-DEC-06 2O07 0 JRNL AUTH H.WU,J.MIN,Y.IKEGUCHI,H.ZENG,A.DONG,P.LOPPNAU,A.E.PEGG, JRNL AUTH 2 A.N.PLOTNIKOV JRNL TITL STRUCTURE AND MECHANISM OF SPERMIDINE SYNTHASES. JRNL REF BIOCHEMISTRY V. 46 8331 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17585781 JRNL DOI 10.1021/BI602498K REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 82.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 42238 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2255 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.89 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2290 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 132 REMARK 3 BIN FREE R VALUE : 0.3790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4427 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 624 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.99000 REMARK 3 B22 (A**2) : -0.20000 REMARK 3 B33 (A**2) : -1.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.42000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.166 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.481 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4588 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6210 ; 1.562 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 556 ; 6.671 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 214 ;37.417 ;24.720 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 777 ;13.386 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.500 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 681 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3469 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2324 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3101 ; 0.300 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 525 ; 0.180 ; 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): 68 ; 0.206 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 28 ; 0.189 ; 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): 2890 ; 0.894 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4505 ; 1.394 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1969 ; 2.403 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1705 ; 3.540 ; 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 : 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 2O07 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000040521. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : VARIMAX REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44511 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 82.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.11900 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2M MG(OAC)2, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K 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 30.33150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 PRO A 3 REMARK 465 GLY A 4 REMARK 465 PRO A 5 REMARK 465 ASP A 6 REMARK 465 GLY A 7 REMARK 465 PRO A 8 REMARK 465 ALA A 9 REMARK 465 ALA A 10 REMARK 465 SER A 11 REMARK 465 GLY A 12 REMARK 465 PRO A 13 REMARK 465 ALA A 14 REMARK 465 ALA A 15 REMARK 465 ASP A 176 REMARK 465 PRO A 177 REMARK 465 MET A 178 REMARK 465 GLY A 179 REMARK 465 PRO A 180 REMARK 465 ALA A 181 REMARK 465 GLU A 182 REMARK 465 SER A 183 REMARK 465 LEU A 184 REMARK 465 PHE A 185 REMARK 465 LYS A 186 REMARK 465 VAL A 301 REMARK 465 SER A 302 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 PRO B 3 REMARK 465 GLY B 4 REMARK 465 PRO B 5 REMARK 465 ASP B 6 REMARK 465 GLY B 7 REMARK 465 PRO B 8 REMARK 465 ALA B 9 REMARK 465 ALA B 10 REMARK 465 SER B 11 REMARK 465 GLY B 12 REMARK 465 PRO B 13 REMARK 465 ALA B 14 REMARK 465 ASP B 300 REMARK 465 VAL B 301 REMARK 465 SER B 302 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 ARG A 17 CD NE CZ NH1 NH2 REMARK 470 GLU A 18 CG CD OE1 OE2 REMARK 470 LYS A 96 CD CE NZ REMARK 470 SER A 175 OG REMARK 470 ARG B 44 CG CD NE CZ NH1 NH2 REMARK 470 MET B 178 CG REMARK 470 GLN B 273 CG CD OE1 NE2 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 628 O HOH B 912 1.92 REMARK 500 O HIS B 42 O HOH B 902 2.01 REMARK 500 N GLU A 187 O HOH A 887 2.14 REMARK 500 O HOH A 666 O HOH A 890 2.14 REMARK 500 O HOH A 888 O HOH A 891 2.19 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 ASN A 93 71.12 -161.10 REMARK 500 GLU A 208 144.81 89.73 REMARK 500 HIS A 213 58.27 -145.06 REMARK 500 ILE A 238 106.14 -167.28 REMARK 500 TYR A 278 -57.20 -124.15 REMARK 500 HIS B 42 -62.13 -141.95 REMARK 500 HIS B 43 89.18 31.21 REMARK 500 ASN B 93 66.42 -157.19 REMARK 500 SER B 175 -167.46 -76.43 REMARK 500 GLU B 208 -176.10 72.54 REMARK 500 LEU B 212 -32.86 -131.76 REMARK 500 ILE B 238 104.53 -170.16 REMARK 500 TYR B 278 -59.60 -124.12 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 SPD A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SPD B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTA B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2O05 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SPERMIDINE SYNTHASE IN COMPLEX WITH 5- REMARK 900 METHYLTHIOADENOSINE REMARK 900 RELATED ID: 2O06 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SPERMIDINE SYNTHASE IN COMPLEX WITH 5- REMARK 900 METHYLTHIOADENOSINE AND 1,4-DIAMINOBUTANE REMARK 900 RELATED ID: 2O0L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN SPERMIDINE SYNTHASE IN COMPLEX WITH REMARK 900 DECARBOXYLATED S-ADENOSYLMETHIONINE DBREF 2O07 A 1 302 UNP P19623 SPEE_HUMAN 1 302 DBREF 2O07 B 1 302 UNP P19623 SPEE_HUMAN 1 302 SEQADV 2O07 GLY A -1 UNP P19623 CLONING ARTIFACT SEQADV 2O07 SER A 0 UNP P19623 CLONING ARTIFACT SEQADV 2O07 GLY B -1 UNP P19623 CLONING ARTIFACT SEQADV 2O07 SER B 0 UNP P19623 CLONING ARTIFACT SEQRES 1 A 304 GLY SER MET GLU PRO GLY PRO ASP GLY PRO ALA ALA SER SEQRES 2 A 304 GLY PRO ALA ALA ILE ARG GLU GLY TRP PHE ARG GLU THR SEQRES 3 A 304 CYS SER LEU TRP PRO GLY GLN ALA LEU SER LEU GLN VAL SEQRES 4 A 304 GLU GLN LEU LEU HIS HIS ARG ARG SER ARG TYR GLN ASP SEQRES 5 A 304 ILE LEU VAL PHE ARG SER LYS THR TYR GLY ASN VAL LEU SEQRES 6 A 304 VAL LEU ASP GLY VAL ILE GLN CYS THR GLU ARG ASP GLU SEQRES 7 A 304 PHE SER TYR GLN GLU MET ILE ALA ASN LEU PRO LEU CYS SEQRES 8 A 304 SER HIS PRO ASN PRO ARG LYS VAL LEU ILE ILE GLY GLY SEQRES 9 A 304 GLY ASP GLY GLY VAL LEU ARG GLU VAL VAL LYS HIS PRO SEQRES 10 A 304 SER VAL GLU SER VAL VAL GLN CYS GLU ILE ASP GLU ASP SEQRES 11 A 304 VAL ILE GLN VAL SER LYS LYS PHE LEU PRO GLY MET ALA SEQRES 12 A 304 ILE GLY TYR SER SER SER LYS LEU THR LEU HIS VAL GLY SEQRES 13 A 304 ASP GLY PHE GLU PHE MET LYS GLN ASN GLN ASP ALA PHE SEQRES 14 A 304 ASP VAL ILE ILE THR ASP SER SER ASP PRO MET GLY PRO SEQRES 15 A 304 ALA GLU SER LEU PHE LYS GLU SER TYR TYR GLN LEU MET SEQRES 16 A 304 LYS THR ALA LEU LYS GLU ASP GLY VAL LEU CYS CYS GLN SEQRES 17 A 304 GLY GLU CYS GLN TRP LEU HIS LEU ASP LEU ILE LYS GLU SEQRES 18 A 304 MET ARG GLN PHE CYS GLN SER LEU PHE PRO VAL VAL ALA SEQRES 19 A 304 TYR ALA TYR CYS THR ILE PRO THR TYR PRO SER GLY GLN SEQRES 20 A 304 ILE GLY PHE MET LEU CYS SER LYS ASN PRO SER THR ASN SEQRES 21 A 304 PHE GLN GLU PRO VAL GLN PRO LEU THR GLN GLN GLN VAL SEQRES 22 A 304 ALA GLN MET GLN LEU LYS TYR TYR ASN SER ASP VAL HIS SEQRES 23 A 304 ARG ALA ALA PHE VAL LEU PRO GLU PHE ALA ARG LYS ALA SEQRES 24 A 304 LEU ASN ASP VAL SER SEQRES 1 B 304 GLY SER MET GLU PRO GLY PRO ASP GLY PRO ALA ALA SER SEQRES 2 B 304 GLY PRO ALA ALA ILE ARG GLU GLY TRP PHE ARG GLU THR SEQRES 3 B 304 CYS SER LEU TRP PRO GLY GLN ALA LEU SER LEU GLN VAL SEQRES 4 B 304 GLU GLN LEU LEU HIS HIS ARG ARG SER ARG TYR GLN ASP SEQRES 5 B 304 ILE LEU VAL PHE ARG SER LYS THR TYR GLY ASN VAL LEU SEQRES 6 B 304 VAL LEU ASP GLY VAL ILE GLN CYS THR GLU ARG ASP GLU SEQRES 7 B 304 PHE SER TYR GLN GLU MET ILE ALA ASN LEU PRO LEU CYS SEQRES 8 B 304 SER HIS PRO ASN PRO ARG LYS VAL LEU ILE ILE GLY GLY SEQRES 9 B 304 GLY ASP GLY GLY VAL LEU ARG GLU VAL VAL LYS HIS PRO SEQRES 10 B 304 SER VAL GLU SER VAL VAL GLN CYS GLU ILE ASP GLU ASP SEQRES 11 B 304 VAL ILE GLN VAL SER LYS LYS PHE LEU PRO GLY MET ALA SEQRES 12 B 304 ILE GLY TYR SER SER SER LYS LEU THR LEU HIS VAL GLY SEQRES 13 B 304 ASP GLY PHE GLU PHE MET LYS GLN ASN GLN ASP ALA PHE SEQRES 14 B 304 ASP VAL ILE ILE THR ASP SER SER ASP PRO MET GLY PRO SEQRES 15 B 304 ALA GLU SER LEU PHE LYS GLU SER TYR TYR GLN LEU MET SEQRES 16 B 304 LYS THR ALA LEU LYS GLU ASP GLY VAL LEU CYS CYS GLN SEQRES 17 B 304 GLY GLU CYS GLN TRP LEU HIS LEU ASP LEU ILE LYS GLU SEQRES 18 B 304 MET ARG GLN PHE CYS GLN SER LEU PHE PRO VAL VAL ALA SEQRES 19 B 304 TYR ALA TYR CYS THR ILE PRO THR TYR PRO SER GLY GLN SEQRES 20 B 304 ILE GLY PHE MET LEU CYS SER LYS ASN PRO SER THR ASN SEQRES 21 B 304 PHE GLN GLU PRO VAL GLN PRO LEU THR GLN GLN GLN VAL SEQRES 22 B 304 ALA GLN MET GLN LEU LYS TYR TYR ASN SER ASP VAL HIS SEQRES 23 B 304 ARG ALA ALA PHE VAL LEU PRO GLU PHE ALA ARG LYS ALA SEQRES 24 B 304 LEU ASN ASP VAL SER HET SPD A 601 10 HET MTA A 501 20 HET SPD B 601 10 HET MTA B 501 20 HETNAM SPD SPERMIDINE HETNAM MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) FORMUL 3 SPD 2(C7 H19 N3) FORMUL 4 MTA 2(C11 H15 N5 O3 S) FORMUL 7 HOH *624(H2 O) HELIX 1 1 GLU A 76 CYS A 89 1 14 HELIX 2 2 GLY A 105 VAL A 112 1 8 HELIX 3 3 ASP A 126 LEU A 137 1 12 HELIX 4 4 LEU A 137 ILE A 142 1 6 HELIX 5 5 GLY A 143 SER A 146 5 4 HELIX 6 6 ASP A 155 GLN A 162 1 8 HELIX 7 7 GLU A 187 ALA A 196 1 10 HELIX 8 8 HIS A 213 PHE A 228 1 16 HELIX 9 9 TYR A 241 SER A 243 5 3 HELIX 10 10 THR A 267 MET A 274 1 8 HELIX 11 11 ASN A 280 ALA A 287 1 8 HELIX 12 12 PRO A 291 ASP A 300 1 10 HELIX 13 13 ASP B 75 CYS B 89 1 15 HELIX 14 14 GLY B 105 VAL B 112 1 8 HELIX 15 15 ASP B 126 LEU B 137 1 12 HELIX 16 16 LEU B 137 ILE B 142 1 6 HELIX 17 17 GLY B 143 SER B 146 5 4 HELIX 18 18 ASP B 155 LYS B 161 1 7 HELIX 19 19 MET B 178 PHE B 185 5 8 HELIX 20 20 LYS B 186 ALA B 196 1 11 HELIX 21 21 HIS B 213 SER B 226 1 14 HELIX 22 22 TYR B 241 SER B 243 5 3 HELIX 23 23 THR B 267 MET B 274 1 8 HELIX 24 24 ASN B 280 ALA B 287 1 8 HELIX 25 25 PRO B 291 ASN B 299 1 9 SHEET 1 A 6 ILE A 16 ARG A 17 0 SHEET 2 A 6 TRP A 20 GLU A 23 -1 O TRP A 20 N ARG A 17 SHEET 3 A 6 GLN A 31 ARG A 47 -1 O LEU A 35 N GLU A 23 SHEET 4 A 6 GLN B 31 ARG B 47 -1 O ALA B 32 N SER A 34 SHEET 5 A 6 TRP B 20 GLU B 23 -1 N GLU B 23 O LEU B 35 SHEET 6 A 6 ILE B 16 ARG B 17 -1 N ARG B 17 O TRP B 20 SHEET 1 B 8 VAL A 68 THR A 72 0 SHEET 2 B 8 ASN A 61 LEU A 65 -1 N LEU A 65 O GLN A 70 SHEET 3 B 8 ASP A 50 SER A 56 -1 N LEU A 52 O VAL A 64 SHEET 4 B 8 GLN A 31 ARG A 47 -1 N GLN A 39 O ARG A 55 SHEET 5 B 8 GLN B 31 ARG B 47 -1 O ALA B 32 N SER A 34 SHEET 6 B 8 ASP B 50 SER B 56 -1 O ARG B 55 N GLN B 39 SHEET 7 B 8 ASN B 61 LEU B 65 -1 O VAL B 64 N LEU B 52 SHEET 8 B 8 VAL B 68 THR B 72 -1 O GLN B 70 N LEU B 65 SHEET 1 C 7 LEU A 151 VAL A 153 0 SHEET 2 C 7 SER A 119 GLU A 124 1 N GLN A 122 O HIS A 152 SHEET 3 C 7 LYS A 96 GLY A 103 1 N ILE A 99 O VAL A 121 SHEET 4 C 7 PHE A 167 ASP A 173 1 O ILE A 171 N ILE A 100 SHEET 5 C 7 LEU A 197 GLU A 208 1 O CYS A 204 N ILE A 170 SHEET 6 C 7 GLN A 245 SER A 252 -1 O GLY A 247 N GLY A 207 SHEET 7 C 7 VAL A 230 THR A 237 -1 N CYS A 236 O ILE A 246 SHEET 1 D 7 LEU B 151 VAL B 153 0 SHEET 2 D 7 SER B 119 GLU B 124 1 N GLN B 122 O HIS B 152 SHEET 3 D 7 LYS B 96 GLY B 103 1 N ILE B 99 O VAL B 121 SHEET 4 D 7 PHE B 167 ASP B 173 1 O ILE B 171 N ILE B 100 SHEET 5 D 7 LEU B 197 GLU B 208 1 O LYS B 198 N PHE B 167 SHEET 6 D 7 GLN B 245 SER B 252 -1 O CYS B 251 N LEU B 203 SHEET 7 D 7 VAL B 230 THR B 237 -1 N ALA B 234 O LEU B 250 SITE 1 AC1 12 GLU A 23 VAL A 68 ILE A 69 GLN A 70 SITE 2 AC1 12 TYR A 79 GLN A 80 ASP A 104 ASP A 173 SITE 3 AC1 12 SER A 174 TYR A 241 PRO A 242 MTA A 501 SITE 1 AC2 13 TRP B 28 VAL B 68 GLN B 70 TYR B 79 SITE 2 AC2 13 GLN B 80 ASP B 104 ASP B 173 SER B 174 SITE 3 AC2 13 ASP B 176 TYR B 241 MTA B 501 HOH B 603 SITE 4 AC2 13 HOH B 605 SITE 1 AC3 15 GLN A 49 LEU A 65 GLY A 101 GLY A 103 SITE 2 AC3 15 ASP A 104 CYS A 123 GLU A 124 ILE A 125 SITE 3 AC3 15 VAL A 129 GLY A 154 ASP A 155 GLY A 156 SITE 4 AC3 15 ASP A 173 SER A 175 SPD A 601 SITE 1 AC4 18 GLN B 49 LEU B 65 GLY B 101 GLY B 103 SITE 2 AC4 18 ASP B 104 CYS B 123 GLU B 124 ILE B 125 SITE 3 AC4 18 ASP B 126 VAL B 129 GLY B 154 ASP B 155 SITE 4 AC4 18 GLY B 156 ASP B 173 PRO B 180 ALA B 181 SITE 5 AC4 18 SER B 183 SPD B 601 CRYST1 58.125 60.663 86.705 90.00 108.68 90.00 P 1 21 1 4 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 0.017204 0.000000 0.005817 0.00000 SCALE2 0.000000 0.016485 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012175 0.00000