HEADER DNA BINDING PROTEIN/DNA 11-NOV-11 3ULP TITLE PLASMODIUM FALCIPARUM SSB COMPLEX WITH SSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SINGLE-STRAND BINDING PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 77-200; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (35-MER); COMPND 8 CHAIN: R, Q; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 5833; SOURCE 4 GENE: PFE0435C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PET21A; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC DNA; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS OB-FOLD, DNA BINDING, SINGLE-STRANDED DNA, APICOPLAST, DNA BINDING KEYWDS 2 PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.ANTONY,T.M.LOHMAN,S.KOROLEV REVDAT 3 13-SEP-23 3ULP 1 REMARK REVDAT 2 25-JUL-12 3ULP 1 JRNL REVDAT 1 09-MAY-12 3ULP 0 JRNL AUTH E.ANTONY,E.A.WEILAND,S.KOROLEV,T.M.LOHMAN JRNL TITL PLASMODIUM FALCIPARUM SSB TETRAMER WRAPS SINGLE-STRANDED DNA JRNL TITL 2 WITH SIMILAR TOPOLOGY BUT OPPOSITE POLARITY TO E. COLI SSB. JRNL REF J.MOL.BIOL. V. 420 269 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22543099 JRNL DOI 10.1016/J.JMB.2012.04.021 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 45791 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2438 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3372 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 185 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3638 REMARK 3 NUCLEIC ACID ATOMS : 1000 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 228 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.10000 REMARK 3 B22 (A**2) : 0.73000 REMARK 3 B33 (A**2) : -1.82000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.193 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.133 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.001 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4812 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6693 ; 1.468 ; 2.216 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 447 ; 9.257 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;39.691 ;23.892 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 691 ;20.654 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;18.668 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 770 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3201 ; 0.019 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2252 ; 2.233 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3617 ; 3.731 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2560 ; 4.727 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3076 ; 6.554 ; 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 3ULP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000068910. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : VHF OPTICS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48456 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.52900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 1EQQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE, PH 8.5, 20 % REMARK 280 PEG 3350, 0.2 M SODIUM BROMIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K 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 59.00850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.39700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.00850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 41.39700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 20700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, R, Q 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 D 229 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 ASN A 169 REMARK 465 ASP A 170 REMARK 465 MET A 171 REMARK 465 ASN A 172 REMARK 465 ASP A 195 REMARK 465 LYS A 196 REMARK 465 ARG A 197 REMARK 465 ASN A 198 REMARK 465 PHE A 199 REMARK 465 ASN A 200 REMARK 465 ASN B 121 REMARK 465 MET B 171 REMARK 465 ASN B 172 REMARK 465 SER B 173 REMARK 465 ASP B 195 REMARK 465 LYS B 196 REMARK 465 ARG B 197 REMARK 465 ASN B 198 REMARK 465 PHE B 199 REMARK 465 ASN B 200 REMARK 465 ASP C 170 REMARK 465 MET C 171 REMARK 465 ASP C 195 REMARK 465 LYS C 196 REMARK 465 ARG C 197 REMARK 465 ASN C 198 REMARK 465 PHE C 199 REMARK 465 ASN C 200 REMARK 465 ASN D 121 REMARK 465 THR D 122 REMARK 465 ASN D 169 REMARK 465 ASP D 170 REMARK 465 MET D 171 REMARK 465 ASP D 195 REMARK 465 LYS D 196 REMARK 465 ARG D 197 REMARK 465 ASN D 198 REMARK 465 PHE D 199 REMARK 465 ASN D 200 REMARK 465 DT R 15 REMARK 465 DT R 16 REMARK 465 DT R 17 REMARK 465 DT R 29 REMARK 465 DT R 30 REMARK 465 DT R 31 REMARK 465 DT R 32 REMARK 465 DT R 33 REMARK 465 DT R 34 REMARK 465 DT R 35 REMARK 465 DT Q 14 REMARK 465 DT Q 15 REMARK 465 DT Q 16 REMARK 465 DT Q 17 REMARK 465 DT Q 30 REMARK 465 DT Q 31 REMARK 465 DT Q 32 REMARK 465 DT Q 33 REMARK 465 DT Q 34 REMARK 465 DT Q 35 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 MET A 77 CG SD CE REMARK 470 PHE A 116 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 174 CG CD OE1 NE2 REMARK 470 TYR A 185 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN A 186 CG OD1 ND2 REMARK 470 MET B 77 CG SD CE REMARK 470 LEU B 100 CB CG CD1 CD2 REMARK 470 PHE B 116 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 118 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 120 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 123 CG OD1 ND2 REMARK 470 ASN B 169 CG OD1 ND2 REMARK 470 ASP B 170 CG OD1 OD2 REMARK 470 TYR B 185 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 187 CG CD CE NZ REMARK 470 MET C 77 CG SD CE REMARK 470 PHE C 116 CG CD1 CD2 CE1 CE2 CZ REMARK 470 THR C 168 OG1 CG2 REMARK 470 ASN C 169 CG OD1 ND2 REMARK 470 GLN C 174 CG CD OE1 NE2 REMARK 470 ASN C 186 CG OD1 ND2 REMARK 470 MET D 77 CG SD CE REMARK 470 ARG D 118 CG CD NE CZ NH1 NH2 REMARK 470 ASP D 119 CG OD1 OD2 REMARK 470 ARG D 120 CG CD NE CZ NH1 NH2 REMARK 470 ASN D 123 CG OD1 ND2 REMARK 470 GLU D 124 CG CD OE1 OE2 REMARK 470 LEU D 125 CG CD1 CD2 REMARK 470 ASN D 172 CG OD1 ND2 REMARK 470 SER D 173 OG REMARK 470 GLN D 174 CG CD OE1 NE2 REMARK 470 TYR D 185 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR D 185 OH REMARK 470 ASN D 186 CB CG OD1 ND2 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 MET D 77 C7 DT Q 11 1.75 REMARK 500 N MET A 77 N3 DT R 27 2.06 REMARK 500 NH2 ARG A 164 O2 DT R 5 2.06 REMARK 500 C7 DT R 18 O HOH R 239 2.07 REMARK 500 NH2 ARG B 164 O2 DT R 22 2.10 REMARK 500 N3 DT R 18 O HOH R 153 2.10 REMARK 500 REMARK 500 REMARK: NULL 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 THR A 122 C7 DT Q 8 4545 1.78 REMARK 500 O THR C 122 C7 DT R 8 4555 1.91 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 C 90 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT R 1 O4' - C4' - C3' ANGL. DEV. = -3.3 DEGREES REMARK 500 DT R 1 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT R 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT R 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT R 7 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT R 8 O4' - C1' - N1 ANGL. DEV. = -5.2 DEGREES REMARK 500 DT R 8 N3 - C4 - O4 ANGL. DEV. = 5.1 DEGREES REMARK 500 DT R 8 C5 - C4 - O4 ANGL. DEV. = -5.9 DEGREES REMARK 500 DT R 13 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT R 18 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DT R 18 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT R 22 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT R 26 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT R 28 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT Q 1 O4' - C4' - C3' ANGL. DEV. = -3.5 DEGREES REMARK 500 DT Q 1 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT Q 2 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT Q 8 O4' - C1' - N1 ANGL. DEV. = -5.8 DEGREES REMARK 500 DT Q 8 N3 - C4 - O4 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT Q 8 C5 - C4 - O4 ANGL. DEV. = -5.3 DEGREES REMARK 500 DT Q 12 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT Q 18 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DT Q 19 C5 - C4 - O4 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT Q 21 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT Q 23 C5 - C4 - O4 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT Q 24 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 DT Q 26 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DT Q 26 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT Q 28 O4' - C1' - N1 ANGL. DEV. = 2.1 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 ASN A 78 -21.31 -146.41 REMARK 500 GLN A 174 83.53 67.24 REMARK 500 LEU A 193 -149.32 -113.14 REMARK 500 ASN B 123 -9.25 58.28 REMARK 500 ASN B 169 115.00 -32.55 REMARK 500 THR C 168 0.32 161.60 REMARK 500 GLN C 174 99.58 78.35 REMARK 500 ASN C 186 4.06 59.11 REMARK 500 LEU C 193 -165.36 -118.20 REMARK 500 GLU D 124 171.66 53.72 REMARK 500 LEU D 125 38.73 95.80 REMARK 500 SER D 173 22.94 -144.77 REMARK 500 TYR D 185 114.19 -38.51 REMARK 500 ASN D 186 -16.43 89.10 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 HIS A 167 THR A 168 48.11 REMARK 500 GLU B 124 LEU B 125 -145.88 REMARK 500 ASN C 121 THR C 122 -149.41 REMARK 500 ASN D 123 GLU D 124 140.42 REMARK 500 GLU D 124 LEU D 125 -39.84 REMARK 500 REMARK 500 REMARK: NULL DBREF 3ULP A 77 200 UNP Q8I415 Q8I415_PLAF7 77 200 DBREF 3ULP B 77 200 UNP Q8I415 Q8I415_PLAF7 77 200 DBREF 3ULP C 77 200 UNP Q8I415 Q8I415_PLAF7 77 200 DBREF 3ULP D 77 200 UNP Q8I415 Q8I415_PLAF7 77 200 DBREF 3ULP R 1 35 PDB 3ULP 3ULP 1 35 DBREF 3ULP Q 1 35 PDB 3ULP 3ULP 1 35 SEQRES 1 A 124 MET ASN GLU LYS SER LEU ASN LYS ILE MET LEU ILE GLY SEQRES 2 A 124 ARG VAL GLY CYS GLU PRO ASP ILE LYS ILE LEU ASN GLY SEQRES 3 A 124 GLY ASP LYS VAL ALA THR PHE SER LEU ALA THR ASN GLU SEQRES 4 A 124 PHE TRP ARG ASP ARG ASN THR ASN GLU LEU LYS SER LYS SEQRES 5 A 124 THR ASP TRP HIS ARG ILE VAL VAL TYR ASP GLN ASN ILE SEQRES 6 A 124 VAL ASP LEU ILE ASP LYS TYR LEU ARG LYS GLY ARG ARG SEQRES 7 A 124 VAL TYR VAL GLN GLY SER LEU HIS THR ARG LYS TRP HIS SEQRES 8 A 124 THR ASN ASP MET ASN SER GLN PRO LYS GLN ILE THR GLU SEQRES 9 A 124 ILE ILE LEU SER TYR ASN LYS GLY ASP LEU ILE PHE LEU SEQRES 10 A 124 ASP ASP LYS ARG ASN PHE ASN SEQRES 1 B 124 MET ASN GLU LYS SER LEU ASN LYS ILE MET LEU ILE GLY SEQRES 2 B 124 ARG VAL GLY CYS GLU PRO ASP ILE LYS ILE LEU ASN GLY SEQRES 3 B 124 GLY ASP LYS VAL ALA THR PHE SER LEU ALA THR ASN GLU SEQRES 4 B 124 PHE TRP ARG ASP ARG ASN THR ASN GLU LEU LYS SER LYS SEQRES 5 B 124 THR ASP TRP HIS ARG ILE VAL VAL TYR ASP GLN ASN ILE SEQRES 6 B 124 VAL ASP LEU ILE ASP LYS TYR LEU ARG LYS GLY ARG ARG SEQRES 7 B 124 VAL TYR VAL GLN GLY SER LEU HIS THR ARG LYS TRP HIS SEQRES 8 B 124 THR ASN ASP MET ASN SER GLN PRO LYS GLN ILE THR GLU SEQRES 9 B 124 ILE ILE LEU SER TYR ASN LYS GLY ASP LEU ILE PHE LEU SEQRES 10 B 124 ASP ASP LYS ARG ASN PHE ASN SEQRES 1 C 124 MET ASN GLU LYS SER LEU ASN LYS ILE MET LEU ILE GLY SEQRES 2 C 124 ARG VAL GLY CYS GLU PRO ASP ILE LYS ILE LEU ASN GLY SEQRES 3 C 124 GLY ASP LYS VAL ALA THR PHE SER LEU ALA THR ASN GLU SEQRES 4 C 124 PHE TRP ARG ASP ARG ASN THR ASN GLU LEU LYS SER LYS SEQRES 5 C 124 THR ASP TRP HIS ARG ILE VAL VAL TYR ASP GLN ASN ILE SEQRES 6 C 124 VAL ASP LEU ILE ASP LYS TYR LEU ARG LYS GLY ARG ARG SEQRES 7 C 124 VAL TYR VAL GLN GLY SER LEU HIS THR ARG LYS TRP HIS SEQRES 8 C 124 THR ASN ASP MET ASN SER GLN PRO LYS GLN ILE THR GLU SEQRES 9 C 124 ILE ILE LEU SER TYR ASN LYS GLY ASP LEU ILE PHE LEU SEQRES 10 C 124 ASP ASP LYS ARG ASN PHE ASN SEQRES 1 D 124 MET ASN GLU LYS SER LEU ASN LYS ILE MET LEU ILE GLY SEQRES 2 D 124 ARG VAL GLY CYS GLU PRO ASP ILE LYS ILE LEU ASN GLY SEQRES 3 D 124 GLY ASP LYS VAL ALA THR PHE SER LEU ALA THR ASN GLU SEQRES 4 D 124 PHE TRP ARG ASP ARG ASN THR ASN GLU LEU LYS SER LYS SEQRES 5 D 124 THR ASP TRP HIS ARG ILE VAL VAL TYR ASP GLN ASN ILE SEQRES 6 D 124 VAL ASP LEU ILE ASP LYS TYR LEU ARG LYS GLY ARG ARG SEQRES 7 D 124 VAL TYR VAL GLN GLY SER LEU HIS THR ARG LYS TRP HIS SEQRES 8 D 124 THR ASN ASP MET ASN SER GLN PRO LYS GLN ILE THR GLU SEQRES 9 D 124 ILE ILE LEU SER TYR ASN LYS GLY ASP LEU ILE PHE LEU SEQRES 10 D 124 ASP ASP LYS ARG ASN PHE ASN SEQRES 1 R 35 DT DT DT DT DT DT DT DT DT DT DT DT DT SEQRES 2 R 35 DT DT DT DT DT DT DT DT DT DT DT DT DT SEQRES 3 R 35 DT DT DT DT DT DT DT DT DT SEQRES 1 Q 35 DT DT DT DT DT DT DT DT DT DT DT DT DT SEQRES 2 Q 35 DT DT DT DT DT DT DT DT DT DT DT DT DT SEQRES 3 Q 35 DT DT DT DT DT DT DT DT DT FORMUL 7 HOH *228(H2 O) HELIX 1 1 ASP A 138 LEU A 149 1 12 HELIX 2 2 ASP B 138 LEU B 149 1 12 HELIX 3 3 ASP C 138 LEU C 149 1 12 HELIX 4 4 ASP D 138 LEU D 149 1 12 SHEET 1 A 5 ASP A 189 PHE A 192 0 SHEET 2 A 5 ARG A 154 TRP A 166 -1 N GLN A 158 O ASP A 189 SHEET 3 A 5 LYS A 176 LEU A 183 -1 O LYS A 176 N TRP A 166 SHEET 4 A 5 LEU A 125 VAL A 136 1 N ARG A 133 O ILE A 181 SHEET 5 A 5 LYS A 105 ARG A 118 -1 N TRP A 117 O LYS A 126 SHEET 1 B 4 ASP A 96 ILE A 99 0 SHEET 2 B 4 LYS A 105 ARG A 118 -1 O VAL A 106 N LYS A 98 SHEET 3 B 4 LEU A 82 VAL A 91 -1 N ARG A 90 O ALA A 112 SHEET 4 B 4 ARG A 154 TRP A 166 -1 O VAL A 157 N LEU A 87 SHEET 1 C 4 LEU A 82 VAL A 91 0 SHEET 2 C 4 LEU B 82 VAL B 91 -1 O MET B 86 N LYS A 84 SHEET 3 C 4 LYS B 105 ARG B 118 -1 O ALA B 112 N ARG B 90 SHEET 4 C 4 ASP B 96 ILE B 99 -1 N LYS B 98 O VAL B 106 SHEET 1 D 7 ASP B 189 ASP B 194 0 SHEET 2 D 7 ARG B 154 TRP B 166 -1 N ARG B 154 O LEU B 193 SHEET 3 D 7 LEU B 82 VAL B 91 -1 N LEU B 87 O VAL B 157 SHEET 4 D 7 LYS B 105 ARG B 118 -1 O ALA B 112 N ARG B 90 SHEET 5 D 7 LEU B 125 VAL B 136 -1 O ASP B 130 N THR B 113 SHEET 6 D 7 LYS B 176 LEU B 183 1 O ILE B 181 N ARG B 133 SHEET 7 D 7 ARG B 154 TRP B 166 -1 N HIS B 162 O GLU B 180 SHEET 1 E 5 ASP C 189 PHE C 192 0 SHEET 2 E 5 ARG C 154 TRP C 166 -1 N TYR C 156 O ILE C 191 SHEET 3 E 5 LYS C 176 LEU C 183 -1 O LYS C 176 N TRP C 166 SHEET 4 E 5 LEU C 125 VAL C 136 1 N ARG C 133 O ILE C 181 SHEET 5 E 5 LYS C 105 ARG C 118 -1 N TRP C 117 O LYS C 126 SHEET 1 F 4 ASP C 96 ILE C 99 0 SHEET 2 F 4 LYS C 105 ARG C 118 -1 O VAL C 106 N LYS C 98 SHEET 3 F 4 LEU C 82 VAL C 91 -1 N ARG C 90 O ALA C 112 SHEET 4 F 4 ARG C 154 TRP C 166 -1 O VAL C 157 N LEU C 87 SHEET 1 G 4 LEU C 82 VAL C 91 0 SHEET 2 G 4 LEU D 82 VAL D 91 -1 O LYS D 84 N MET C 86 SHEET 3 G 4 LYS D 105 TRP D 117 -1 O ALA D 112 N ARG D 90 SHEET 4 G 4 ASP D 96 ILE D 99 -1 N LYS D 98 O VAL D 106 SHEET 1 H 7 ASP D 189 PHE D 192 0 SHEET 2 H 7 ARG D 154 HIS D 167 -1 N TYR D 156 O ILE D 191 SHEET 3 H 7 LEU D 82 VAL D 91 -1 N LEU D 87 O VAL D 157 SHEET 4 H 7 LYS D 105 TRP D 117 -1 O ALA D 112 N ARG D 90 SHEET 5 H 7 LYS D 126 VAL D 136 -1 O VAL D 136 N ALA D 107 SHEET 6 H 7 PRO D 175 LEU D 183 1 O ILE D 181 N ARG D 133 SHEET 7 H 7 ARG D 154 HIS D 167 -1 N SER D 160 O ILE D 182 CISPEP 1 HIS C 167 THR C 168 0 -5.28 CISPEP 2 THR C 168 ASN C 169 0 -4.83 CRYST1 118.017 82.794 87.556 90.00 99.57 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 0.008473 0.000000 0.001428 0.00000 SCALE2 0.000000 0.012078 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011582 0.00000