HEADER TRANSPORT PROTEIN 01-JUL-25 9PDZ TITLE CRYSTAL STRUCTURE OF A SPERMIDINE BINDING PROTEIN ISOLATED FROM TITLE 2 SYNECHOCOCCUS CC9311 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PERIPLASMIC BINDING PROTEIN-LIKE II SUPERFAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS SP. CC9311; SOURCE 3 ORGANISM_TAXID: 64471; SOURCE 4 GENE: SYNC_2119; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: LEMO21 KEYWDS SUBSTRATE-BINDING PROTEIN, MARINE CYANOBACTERIA, SPERMIDINE-BINDING KEYWDS 2 PROTEIN, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.S.SHAH,C.M.ORR,H.MIKOLAJEK,V.MYKHAYLYK,R.J.OWENS,I.T.PAULSEN REVDAT 1 22-JUL-26 9PDZ 0 JRNL AUTH B.S.SHAH,H.MIKOLAJEK,V.MYKHAYLYK,C.M.ORR,R.J.OWENS, JRNL AUTH 2 I.T.PAULSEN JRNL TITL CRYSTAL STRUCTURE OF A SPERMIDINE BINDING PROTEIN ISOLATED JRNL TITL 2 FROM SYNECHOCOCCUS CC9311 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 (REFMACAT 0.4.105) REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 3 NUMBER OF REFLECTIONS : 27216 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.857 REMARK 3 FREE R VALUE TEST SET COUNT : 1322 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1354 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.4400 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.4400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2261 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 234 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.13100 REMARK 3 B22 (A**2) : 0.87900 REMARK 3 B33 (A**2) : 0.11600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.42800 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.145 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.133 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.096 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.267 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2506 ; 0.016 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2430 ; 0.003 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3427 ; 2.343 ; 1.807 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5616 ; 0.892 ; 1.742 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 320 ; 6.804 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 19 ;17.603 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 403 ;14.450 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 377 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3018 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 564 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 507 ; 0.225 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 34 ; 0.196 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1162 ; 0.169 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 191 ; 0.176 ; 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1244 ; 3.075 ; 2.270 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1244 ; 3.073 ; 2.270 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1576 ; 4.204 ; 4.067 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1577 ; 4.202 ; 4.068 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1262 ; 4.639 ; 2.751 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1263 ; 4.637 ; 2.752 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1851 ; 6.440 ; 4.778 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1852 ; 6.439 ; 4.778 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : Ap 2 Ap 295 REMARK 3 ORIGIN FOR THE GROUP (A): 10.0587 18.5811 48.2071 REMARK 3 T TENSOR REMARK 3 T11: 0.0348 T22: 0.0382 REMARK 3 T33: 0.0170 T12: -0.0039 REMARK 3 T13: 0.0024 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 1.3553 L22: 3.0219 REMARK 3 L33: 0.9245 L12: -0.2787 REMARK 3 L13: -0.3842 L23: 0.0280 REMARK 3 S TENSOR REMARK 3 S11: 0.0175 S12: 0.2212 S13: 0.0372 REMARK 3 S21: -0.1905 S22: -0.0395 S23: 0.0685 REMARK 3 S31: -0.1053 S32: -0.0447 S33: 0.0220 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9PDZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1000296359. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-20; 26-JUN-20; 26-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 80; 80; 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; Y REMARK 200 RADIATION SOURCE : DIAMOND; DIAMOND; DIAMOND REMARK 200 BEAMLINE : I23; I23; I23 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M; M REMARK 200 WAVELENGTH OR RANGE (A) : 2.7552; 4.2753; 4.5082 REMARK 200 MONOCHROMATOR : SI(111); SI(111); SI(111) REMARK 200 OPTICS : NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; PIXEL; PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 12M; DECTRIS REMARK 200 PILATUS 12M; DECTRIS PILATUS 12M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27220 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.796 REMARK 200 RESOLUTION RANGE LOW (A) : 45.847 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH; SINGLE REMARK 200 WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CRANK2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 8000, 100 MM HEPES/ REMARK 280 SODIUM HYDROXIDE PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K 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 32.99000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU A 106A REMARK 465 PRO A 106B REMARK 465 ALA A 106C REMARK 465 LEU A 106D REMARK 465 LYS A 106E REMARK 465 ASP A 106F REMARK 465 GLN A 106G REMARK 465 ALA A 106H REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 10 CG CD CE NZ REMARK 470 LYS A 18 CG CD CE NZ REMARK 470 GLU A 268 CG CD OE1 OE2 REMARK 470 ASP A 280 CG OD1 OD2 REMARK 470 ASP A 285 CG OD1 OD2 REMARK 470 LYS A 288 CG CD CE NZ REMARK 470 LYS A 292 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 H HIS A 161 O HOH A 403 1.34 REMARK 500 HE ARG A 6 OG1 THR A 43 1.55 REMARK 500 NZ LYS A 21 O HOH A 401 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 105 CG - CD - NE ANGL. DEV. = -15.3 DEGREES REMARK 500 ARG A 132 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 132 NE - CZ - NH1 ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 132 NE - CZ - NH2 ANGL. DEV. = -10.2 DEGREES REMARK 500 MET A 141 CG - SD - CE ANGL. DEV. = -12.2 DEGREES REMARK 500 ASP A 159 CB - CA - C ANGL. DEV. = 14.9 DEGREES REMARK 500 ARG A 209 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 233 N - CA - CB ANGL. DEV. = -12.8 DEGREES REMARK 500 ARG A 254 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES 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 66 55.97 -143.69 REMARK 500 ASN A 111 50.20 -96.27 REMARK 500 ASP A 158 125.95 179.38 REMARK 500 PRO A 242 38.58 -76.67 REMARK 500 LEU A 276 73.45 -118.53 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 ASP A 159 ARG A 160 -142.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 25 0.15 SIDE CHAIN REMARK 500 ARG A 132 0.09 SIDE CHAIN REMARK 500 ARG A 148 0.14 SIDE CHAIN REMARK 500 ARG A 149 0.10 SIDE CHAIN REMARK 500 ARG A 160 0.10 SIDE CHAIN REMARK 500 ARG A 233 0.08 SIDE CHAIN REMARK 500 ARG A 254 0.25 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 9PDZ A 2 295 UNP Q0I8A1 Q0I8A1_SYNS3 39 337 SEQRES 1 A 299 SER PRO ILE MET ARG ALA PRO THR LYS THR LEU PRO ALA SEQRES 2 A 299 PRO TRP GLN LYS GLN LEU LYS ALA PRO TRP ARG ILE THR SEQRES 3 A 299 GLU LEU LYS ALA PHE VAL SER SER ASP PRO PRO TRP LEU SEQRES 4 A 299 SER SER THR ASP LEU LEU THR ILE GLY ASP GLY TRP LEU SEQRES 5 A 299 SER ASN LEU ASN PRO GLY SER PHE GLN ALA ILE ASP ALA SEQRES 6 A 299 ALA PRO LEU GLN SER GLN LEU GLY PRO LEU ALA GLU GLN SEQRES 7 A 299 PHE LEU SER GLU LEU PRO THR SER TRP LYS GLY LYS ILE SEQRES 8 A 299 PHE PRO VAL GLY VAL SER PRO TRP VAL LEU LEU PHE ARG SEQRES 9 A 299 GLY GLU PRO ALA LEU LYS ASP GLN ALA SER ASN SER TRP SEQRES 10 A 299 ASP VAL LEU LEU ASP PRO GLU PHE LYS GLY LYS VAL LEU SEQRES 11 A 299 LEU PRO SER SER PRO ARG LEU VAL MET SER LEU ALA GLU SEQRES 12 A 299 HIS MET GLN THR PRO ASP ALA LEU ARG ARG LEU ARG GLN SEQRES 13 A 299 ALA ALA ILE SER PHE ASP ASP ARG HIS ALA LEU ASN TRP SEQRES 14 A 299 LEU LEU GLN GLY ASP ALA GLN VAL ALA VAL LEU PRO LEU SEQRES 15 A 299 GLN ARG SER MET GLY ALA LEU LEU ARG ASP GLN ARG LEU SEQRES 16 A 299 HIS ALA VAL LEU PRO ALA GLN GLY ALA PRO LEU ASN TRP SEQRES 17 A 299 THR LEU MET LEU ARG PRO SER SER SER LYS GLU PRO LEU SEQRES 18 A 299 PRO GLN ASP TRP VAL LYS LYS ALA TRP GLU GLU PRO LEU SEQRES 19 A 299 LEU SER ARG LEU LEU SER ALA GLY TRP VAL PRO PRO LEU SEQRES 20 A 299 ALA ARG SER LYS LEU SER THR ALA MET SER ARG VAL PRO SEQRES 21 A 299 LYS ARG LEU HIS ALA LEU VAL LEU PRO SER ASN GLU ILE SEQRES 22 A 299 TRP GLN SER CYS TRP ASN LEU ALA PRO LEU ASP PRO SER SEQRES 23 A 299 GLU GLN ASP ALA LEU LYS ALA LYS TRP LYS ALA SER ALA HET EDO A 301 8 HET EDO A 302 8 HET EDO A 303 8 HET EDO A 304 8 HET EDO A 305 8 HET EDO A 306 8 HET EDO A 307 8 HET SPD A 308 24 HET EDO A 309 8 HET CL A 310 1 HET CL A 311 1 HET CL A 312 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM SPD SPERMIDINE HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL HETSYN SPD N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) FORMUL 2 EDO 8(C2 H6 O2) FORMUL 9 SPD C7 H19 N3 FORMUL 11 CL 3(CL 1-) FORMUL 14 HOH *234(H2 O) HELIX 1 AA1 PRO A 13 LYS A 18 1 6 HELIX 2 AA2 PRO A 37 THR A 43 5 7 HELIX 3 AA3 GLY A 51 LEU A 56 5 6 HELIX 4 AA4 ASN A 57 GLY A 59 5 3 HELIX 5 AA5 ALA A 66 SER A 71 1 6 HELIX 6 AA6 GLY A 74 GLU A 83 1 10 HELIX 7 AA7 LEU A 84 LYS A 89 5 6 HELIX 8 AA8 SER A 112 LYS A 122 5 11 HELIX 9 AA9 SER A 130 HIS A 140 1 11 HELIX 10 AB1 ASP A 145 ALA A 153 1 9 HELIX 11 AB2 HIS A 161 GLY A 169 1 9 HELIX 12 AB3 LEU A 178 ASP A 188 1 11 HELIX 13 AB4 PRO A 218 ALA A 225 1 8 HELIX 14 AB5 PRO A 229 ALA A 237 1 9 HELIX 15 AB6 ALA A 244 THR A 250 1 7 HELIX 16 AB7 PRO A 256 ARG A 258 5 3 HELIX 17 AB8 LEU A 259 LEU A 264 1 6 HELIX 18 AB9 SER A 266 CYS A 273 1 8 HELIX 19 AC1 ASP A 280 SER A 294 1 15 SHEET 1 AA1 8 ARG A 25 GLU A 28 0 SHEET 2 AA1 8 ILE A 4 ALA A 7 1 N MET A 5 O ARG A 25 SHEET 3 AA1 8 LEU A 45 GLY A 49 1 O THR A 47 N ARG A 6 SHEET 4 AA1 8 LEU A 202 PRO A 210 -1 O LEU A 206 N ILE A 48 SHEET 5 AA1 8 PHE A 93 ARG A 105 -1 N VAL A 95 O THR A 205 SHEET 6 AA1 8 VAL A 173 PRO A 177 -1 O ALA A 174 N LEU A 103 SHEET 7 AA1 8 VAL A 125 LEU A 127 1 N LEU A 126 O VAL A 173 SHEET 8 AA1 8 ALA A 154 PHE A 157 1 O ILE A 155 N VAL A 125 SHEET 1 AA2 4 PHE A 61 GLN A 62 0 SHEET 2 AA2 4 LEU A 202 PRO A 210 -1 O ARG A 209 N GLN A 62 SHEET 3 AA2 4 PHE A 93 ARG A 105 -1 N VAL A 95 O THR A 205 SHEET 4 AA2 4 LEU A 191 VAL A 194 -1 O HIS A 192 N PHE A 104 CISPEP 1 ALA A 22 PRO A 23 0 10.94 CISPEP 2 GLU A 228 PRO A 229 0 5.68 CRYST1 39.080 65.980 64.370 90.00 98.63 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.025589 0.000000 0.003885 0.00000 SCALE2 0.000000 0.015156 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015713 0.00000 CONECT 4768 4769 4770 4772 4773 CONECT 4769 4768 CONECT 4770 4768 4771 4774 4775 CONECT 4771 4770 CONECT 4772 4768 CONECT 4773 4768 CONECT 4774 4770 CONECT 4775 4770 CONECT 4776 4777 4778 4780 4781 CONECT 4777 4776 CONECT 4778 4776 4779 4782 4783 CONECT 4779 4778 CONECT 4780 4776 CONECT 4781 4776 CONECT 4782 4778 CONECT 4783 4778 CONECT 4784 4785 4786 4788 4789 CONECT 4785 4784 CONECT 4786 4784 4787 4790 4791 CONECT 4787 4786 CONECT 4788 4784 CONECT 4789 4784 CONECT 4790 4786 CONECT 4791 4786 CONECT 4792 4793 4794 4796 4797 CONECT 4793 4792 CONECT 4794 4792 4795 4798 4799 CONECT 4795 4794 CONECT 4796 4792 CONECT 4797 4792 CONECT 4798 4794 CONECT 4799 4794 CONECT 4800 4801 4802 4804 4805 CONECT 4801 4800 CONECT 4802 4800 4803 4806 4807 CONECT 4803 4802 CONECT 4804 4800 CONECT 4805 4800 CONECT 4806 4802 CONECT 4807 4802 CONECT 4808 4809 4810 4812 4813 CONECT 4809 4808 CONECT 4810 4808 4811 4814 4815 CONECT 4811 4810 CONECT 4812 4808 CONECT 4813 4808 CONECT 4814 4810 CONECT 4815 4810 CONECT 4816 4817 4818 4820 4821 CONECT 4817 4816 CONECT 4818 4816 4819 4822 4823 CONECT 4819 4818 CONECT 4820 4816 CONECT 4821 4816 CONECT 4822 4818 CONECT 4823 4818 CONECT 4824 4825 CONECT 4825 4824 4826 4834 4835 CONECT 4826 4825 4827 4836 4837 CONECT 4827 4826 4828 4838 4839 CONECT 4828 4827 4829 4840 4841 CONECT 4829 4828 4830 CONECT 4830 4829 4831 4842 4843 CONECT 4831 4830 4832 4844 4845 CONECT 4832 4831 4833 4846 4847 CONECT 4833 4832 CONECT 4834 4825 CONECT 4835 4825 CONECT 4836 4826 CONECT 4837 4826 CONECT 4838 4827 CONECT 4839 4827 CONECT 4840 4828 CONECT 4841 4828 CONECT 4842 4830 CONECT 4843 4830 CONECT 4844 4831 CONECT 4845 4831 CONECT 4846 4832 CONECT 4847 4832 CONECT 4848 4849 4850 4852 4853 CONECT 4849 4848 CONECT 4850 4848 4851 4854 4855 CONECT 4851 4850 CONECT 4852 4848 CONECT 4853 4848 CONECT 4854 4850 CONECT 4855 4850 MASTER 369 0 12 19 12 0 0 6 2540 1 88 23 END