HEADER TOXIN 22-JUL-08 3DWA TITLE CRYSTAL STRUCTURE OF THE B-SUBUNIT OF THE AB5 TOXIN FROM E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUBTILASE CYTOTOXIN, SUBUNIT B; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 FRAGMENT: RESIDUES IN DATABASE 24-141; COMPND 5 SYNONYM: SUBB; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: SUBB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR E.BYRES,A.W.PATON,J.C.PATON,J.C.LOFLING,D.F.SMITH,M.C.J.WILCE, AUTHOR 2 U.M.TALBOT,D.C.CHONG,H.YU,S.HUANG,X.CHEN,N.M.VARKI,A.VARKI, AUTHOR 3 J.ROSSJOHN,T.BEDDOE REVDAT 3 30-OCT-24 3DWA 1 REMARK SEQADV LINK REVDAT 2 09-DEC-08 3DWA 1 JRNL VERSN REVDAT 1 04-NOV-08 3DWA 0 JRNL AUTH E.BYRES,A.W.PATON,J.C.PATON,J.C.LOFLING,D.F.SMITH, JRNL AUTH 2 M.C.J.WILCE,U.M.TALBOT,D.C.CHONG,H.YU,S.HUANG,X.CHEN, JRNL AUTH 3 N.M.VARKI,A.VARKI,J.ROSSJOHN,T.BEDDOE JRNL TITL INCORPORATION OF A NON-HUMAN GLYCAN MEDIATES HUMAN JRNL TITL 2 SUSCEPTIBILITY TO A BACTERIAL TOXIN JRNL REF NATURE V. 456 648 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18971931 JRNL DOI 10.1038/NATURE07428 REMARK 2 REMARK 2 RESOLUTION. 2.08 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) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.0 REMARK 3 NUMBER OF REFLECTIONS : 43610 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2361 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) : 2.08 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.14 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2622 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 144 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4546 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 80 REMARK 3 SOLVENT ATOMS : 340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.98000 REMARK 3 B22 (A**2) : -0.98000 REMARK 3 B33 (A**2) : 1.48000 REMARK 3 B12 (A**2) : -0.49000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.192 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.177 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.107 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.912 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4758 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6442 ; 1.702 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 583 ; 8.387 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 195 ;36.235 ;23.846 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 705 ;16.597 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;15.297 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 679 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3592 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2193 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3257 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 321 ; 0.167 ; 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): 38 ; 0.273 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.128 ; 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): 2978 ; 1.393 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4699 ; 2.045 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2104 ; 3.011 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1743 ; 4.293 ; 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: NULL REMARK 4 REMARK 4 3DWA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048568. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45985 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.084 REMARK 200 RESOLUTION RANGE LOW (A) : 84.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 2.08 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16%(W/V) PEG 3350, 100MM SODIUM REMARK 280 CACODYLATE, 200MM AMMONIUM FLUORIDE, PH 6.2, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 110.24000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.12000 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 82.68000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 27.56000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 137.80000 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 LEU A 119 REMARK 465 GLU A 120 REMARK 465 HIS A 121 REMARK 465 HIS A 122 REMARK 465 HIS A 123 REMARK 465 HIS A 124 REMARK 465 HIS A 125 REMARK 465 HIS A 126 REMARK 465 SER B 118 REMARK 465 LEU B 119 REMARK 465 GLU B 120 REMARK 465 HIS B 121 REMARK 465 HIS B 122 REMARK 465 HIS B 123 REMARK 465 HIS B 124 REMARK 465 HIS B 125 REMARK 465 HIS B 126 REMARK 465 HIS C 121 REMARK 465 HIS C 122 REMARK 465 HIS C 123 REMARK 465 HIS C 124 REMARK 465 HIS C 125 REMARK 465 HIS C 126 REMARK 465 SER D 118 REMARK 465 LEU D 119 REMARK 465 GLU D 120 REMARK 465 HIS D 121 REMARK 465 HIS D 122 REMARK 465 HIS D 123 REMARK 465 HIS D 124 REMARK 465 HIS D 125 REMARK 465 HIS D 126 REMARK 465 ASN E 117 REMARK 465 SER E 118 REMARK 465 LEU E 119 REMARK 465 GLU E 120 REMARK 465 HIS E 121 REMARK 465 HIS E 122 REMARK 465 HIS E 123 REMARK 465 HIS E 124 REMARK 465 HIS E 125 REMARK 465 HIS E 126 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLN C 72 CB GLN C 72 CG -0.204 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 ALA C 38 N - CA - C ANGL. DEV. = -23.3 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 SER A 51 -70.58 -64.79 REMARK 500 LEU A 92 -98.95 -123.33 REMARK 500 THR A 105 -166.47 -126.10 REMARK 500 ALA B 38 -112.39 46.89 REMARK 500 ASN B 49 15.01 59.02 REMARK 500 LEU B 92 -99.78 -124.26 REMARK 500 SER C 37 -38.32 -33.43 REMARK 500 ALA C 38 -17.46 -140.22 REMARK 500 SER C 50 -162.65 -62.65 REMARK 500 SER C 51 -128.35 -50.14 REMARK 500 LEU C 92 -99.00 -121.07 REMARK 500 ALA D 38 1.44 -67.30 REMARK 500 SER D 51 179.24 75.59 REMARK 500 LEU D 92 -94.49 -123.85 REMARK 500 GLN E 36 169.09 131.06 REMARK 500 LEU E 92 -89.97 -121.75 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 SER C 37 ALA C 38 -104.63 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 1PE A 127 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE B 127 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE C 127 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE D 127 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE E 127 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DWP RELATED DB: PDB REMARK 900 RELATED ID: 3DWQ RELATED DB: PDB DBREF 3DWA A 1 118 UNP Q3ZTX8 Q3ZTX8_ECOLX 24 141 DBREF 3DWA B 1 118 UNP Q3ZTX8 Q3ZTX8_ECOLX 24 141 DBREF 3DWA C 1 118 UNP Q3ZTX8 Q3ZTX8_ECOLX 24 141 DBREF 3DWA D 1 118 UNP Q3ZTX8 Q3ZTX8_ECOLX 24 141 DBREF 3DWA E 1 118 UNP Q3ZTX8 Q3ZTX8_ECOLX 24 141 SEQADV 3DWA LEU A 119 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA GLU A 120 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS A 121 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS A 122 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS A 123 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS A 124 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS A 125 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS A 126 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA LEU B 119 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA GLU B 120 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS B 121 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS B 122 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS B 123 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS B 124 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS B 125 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS B 126 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA LEU C 119 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA GLU C 120 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS C 121 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS C 122 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS C 123 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS C 124 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS C 125 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS C 126 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA LEU D 119 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA GLU D 120 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS D 121 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS D 122 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS D 123 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS D 124 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS D 125 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS D 126 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA LEU E 119 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA GLU E 120 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS E 121 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS E 122 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS E 123 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS E 124 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS E 125 UNP Q3ZTX8 EXPRESSION TAG SEQADV 3DWA HIS E 126 UNP Q3ZTX8 EXPRESSION TAG SEQRES 1 A 126 GLU TRP THR GLY ASP ALA ARG ASP GLY MSE PHE SER GLY SEQRES 2 A 126 VAL VAL ILE THR GLN PHE HIS THR GLY GLN ILE ASP ASN SEQRES 3 A 126 LYS PRO TYR PHE CYS ILE GLU GLY LYS GLN SER ALA GLY SEQRES 4 A 126 SER SER ILE SER ALA CYS SER MSE LYS ASN SER SER VAL SEQRES 5 A 126 TRP GLY ALA SER PHE SER THR LEU TYR ASN GLN ALA LEU SEQRES 6 A 126 TYR PHE TYR THR THR GLY GLN PRO VAL ARG ILE TYR TYR SEQRES 7 A 126 GLU PRO GLY VAL TRP THR TYR PRO PRO PHE VAL LYS ALA SEQRES 8 A 126 LEU THR SER ASN ALA LEU VAL GLY LEU SER THR CYS THR SEQRES 9 A 126 THR SER THR GLU CYS PHE GLY PRO ASP ARG LYS LYS ASN SEQRES 10 A 126 SER LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 126 GLU TRP THR GLY ASP ALA ARG ASP GLY MSE PHE SER GLY SEQRES 2 B 126 VAL VAL ILE THR GLN PHE HIS THR GLY GLN ILE ASP ASN SEQRES 3 B 126 LYS PRO TYR PHE CYS ILE GLU GLY LYS GLN SER ALA GLY SEQRES 4 B 126 SER SER ILE SER ALA CYS SER MSE LYS ASN SER SER VAL SEQRES 5 B 126 TRP GLY ALA SER PHE SER THR LEU TYR ASN GLN ALA LEU SEQRES 6 B 126 TYR PHE TYR THR THR GLY GLN PRO VAL ARG ILE TYR TYR SEQRES 7 B 126 GLU PRO GLY VAL TRP THR TYR PRO PRO PHE VAL LYS ALA SEQRES 8 B 126 LEU THR SER ASN ALA LEU VAL GLY LEU SER THR CYS THR SEQRES 9 B 126 THR SER THR GLU CYS PHE GLY PRO ASP ARG LYS LYS ASN SEQRES 10 B 126 SER LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 C 126 GLU TRP THR GLY ASP ALA ARG ASP GLY MSE PHE SER GLY SEQRES 2 C 126 VAL VAL ILE THR GLN PHE HIS THR GLY GLN ILE ASP ASN SEQRES 3 C 126 LYS PRO TYR PHE CYS ILE GLU GLY LYS GLN SER ALA GLY SEQRES 4 C 126 SER SER ILE SER ALA CYS SER MSE LYS ASN SER SER VAL SEQRES 5 C 126 TRP GLY ALA SER PHE SER THR LEU TYR ASN GLN ALA LEU SEQRES 6 C 126 TYR PHE TYR THR THR GLY GLN PRO VAL ARG ILE TYR TYR SEQRES 7 C 126 GLU PRO GLY VAL TRP THR TYR PRO PRO PHE VAL LYS ALA SEQRES 8 C 126 LEU THR SER ASN ALA LEU VAL GLY LEU SER THR CYS THR SEQRES 9 C 126 THR SER THR GLU CYS PHE GLY PRO ASP ARG LYS LYS ASN SEQRES 10 C 126 SER LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 D 126 GLU TRP THR GLY ASP ALA ARG ASP GLY MSE PHE SER GLY SEQRES 2 D 126 VAL VAL ILE THR GLN PHE HIS THR GLY GLN ILE ASP ASN SEQRES 3 D 126 LYS PRO TYR PHE CYS ILE GLU GLY LYS GLN SER ALA GLY SEQRES 4 D 126 SER SER ILE SER ALA CYS SER MSE LYS ASN SER SER VAL SEQRES 5 D 126 TRP GLY ALA SER PHE SER THR LEU TYR ASN GLN ALA LEU SEQRES 6 D 126 TYR PHE TYR THR THR GLY GLN PRO VAL ARG ILE TYR TYR SEQRES 7 D 126 GLU PRO GLY VAL TRP THR TYR PRO PRO PHE VAL LYS ALA SEQRES 8 D 126 LEU THR SER ASN ALA LEU VAL GLY LEU SER THR CYS THR SEQRES 9 D 126 THR SER THR GLU CYS PHE GLY PRO ASP ARG LYS LYS ASN SEQRES 10 D 126 SER LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 E 126 GLU TRP THR GLY ASP ALA ARG ASP GLY MSE PHE SER GLY SEQRES 2 E 126 VAL VAL ILE THR GLN PHE HIS THR GLY GLN ILE ASP ASN SEQRES 3 E 126 LYS PRO TYR PHE CYS ILE GLU GLY LYS GLN SER ALA GLY SEQRES 4 E 126 SER SER ILE SER ALA CYS SER MSE LYS ASN SER SER VAL SEQRES 5 E 126 TRP GLY ALA SER PHE SER THR LEU TYR ASN GLN ALA LEU SEQRES 6 E 126 TYR PHE TYR THR THR GLY GLN PRO VAL ARG ILE TYR TYR SEQRES 7 E 126 GLU PRO GLY VAL TRP THR TYR PRO PRO PHE VAL LYS ALA SEQRES 8 E 126 LEU THR SER ASN ALA LEU VAL GLY LEU SER THR CYS THR SEQRES 9 E 126 THR SER THR GLU CYS PHE GLY PRO ASP ARG LYS LYS ASN SEQRES 10 E 126 SER LEU GLU HIS HIS HIS HIS HIS HIS MODRES 3DWA MSE A 10 MET SELENOMETHIONINE MODRES 3DWA MSE A 47 MET SELENOMETHIONINE MODRES 3DWA MSE B 10 MET SELENOMETHIONINE MODRES 3DWA MSE B 47 MET SELENOMETHIONINE MODRES 3DWA MSE C 10 MET SELENOMETHIONINE MODRES 3DWA MSE C 47 MET SELENOMETHIONINE MODRES 3DWA MSE D 10 MET SELENOMETHIONINE MODRES 3DWA MSE D 47 MET SELENOMETHIONINE MODRES 3DWA MSE E 10 MET SELENOMETHIONINE MODRES 3DWA MSE E 47 MET SELENOMETHIONINE HET MSE A 10 8 HET MSE A 47 8 HET MSE B 10 8 HET MSE B 47 8 HET MSE C 10 8 HET MSE C 47 8 HET MSE D 10 8 HET MSE D 47 8 HET MSE E 10 8 HET MSE E 47 8 HET 1PE A 127 16 HET 1PE B 127 16 HET 1PE C 127 16 HET 1PE D 127 16 HET 1PE E 127 16 HETNAM MSE SELENOMETHIONINE HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 1 MSE 10(C5 H11 N O2 SE) FORMUL 6 1PE 5(C10 H22 O6) FORMUL 11 HOH *340(H2 O) HELIX 1 1 TRP A 53 ALA A 55 5 3 HELIX 2 2 SER A 56 GLY A 71 1 16 HELIX 3 3 TYR A 85 LEU A 92 1 8 HELIX 4 4 TRP B 53 ALA B 55 5 3 HELIX 5 5 SER B 56 GLY B 71 1 16 HELIX 6 6 TYR B 85 LEU B 92 1 8 HELIX 7 7 TRP C 53 ALA C 55 5 3 HELIX 8 8 SER C 56 GLY C 71 1 16 HELIX 9 9 TYR C 85 LEU C 92 1 8 HELIX 10 10 SER D 51 ALA D 55 5 5 HELIX 11 11 SER D 56 GLY D 71 1 16 HELIX 12 12 TYR D 85 LEU D 92 1 8 HELIX 13 13 TRP E 53 ALA E 55 5 3 HELIX 14 14 SER E 56 GLY E 71 1 16 HELIX 15 15 TYR E 85 LEU E 92 1 8 SHEET 1 A15 MSE A 10 ILE A 24 0 SHEET 2 A15 LYS A 27 LYS A 35 -1 O CYS A 31 N HIS A 20 SHEET 3 A15 SER A 41 MSE A 47 -1 O SER A 46 N PHE A 30 SHEET 4 A15 ALA A 96 THR A 102 1 O LEU A 97 N CYS A 45 SHEET 5 A15 VAL A 74 GLU A 79 -1 N ARG A 75 O SER A 101 SHEET 6 A15 MSE A 10 ILE A 24 -1 N PHE A 11 O ILE A 76 SHEET 7 A15 ALA E 96 THR E 102 -1 O LEU E 100 N THR A 21 SHEET 8 A15 VAL E 74 GLU E 79 -1 N TYR E 77 O VAL E 98 SHEET 9 A15 MSE E 10 ILE E 24 -1 N VAL E 14 O VAL E 74 SHEET 10 A15 ALA B 96 THR B 102 -1 N THR B 102 O PHE E 19 SHEET 11 A15 SER B 41 MSE B 47 1 N CYS B 45 O LEU B 97 SHEET 12 A15 LYS B 27 LYS B 35 -1 N ILE B 32 O ALA B 44 SHEET 13 A15 MSE B 10 ILE B 24 -1 N THR B 17 O GLU B 33 SHEET 14 A15 VAL B 74 GLU B 79 -1 O VAL B 74 N VAL B 14 SHEET 15 A15 ALA B 96 THR B 102 -1 O VAL B 98 N TYR B 77 SHEET 1 B16 MSE E 10 ILE E 24 0 SHEET 2 B16 LYS E 27 LYS E 35 -1 O CYS E 31 N HIS E 20 SHEET 3 B16 SER E 41 MSE E 47 -1 O SER E 46 N PHE E 30 SHEET 4 B16 ALA E 96 THR E 102 1 O LEU E 97 N CYS E 45 SHEET 5 B16 VAL E 74 GLU E 79 -1 N TYR E 77 O VAL E 98 SHEET 6 B16 MSE E 10 ILE E 24 -1 N VAL E 14 O VAL E 74 SHEET 7 B16 ALA B 96 THR B 102 -1 N THR B 102 O PHE E 19 SHEET 8 B16 SER B 41 MSE B 47 1 N CYS B 45 O LEU B 97 SHEET 9 B16 LYS B 27 LYS B 35 -1 N ILE B 32 O ALA B 44 SHEET 10 B16 MSE B 10 ILE B 24 -1 N THR B 17 O GLU B 33 SHEET 11 B16 ALA D 96 THR D 102 -1 O LEU D 100 N THR B 21 SHEET 12 B16 PRO D 73 GLU D 79 -1 N TYR D 77 O VAL D 98 SHEET 13 B16 MSE D 10 ILE D 24 -1 N VAL D 14 O VAL D 74 SHEET 14 B16 ALA C 96 THR C 102 -1 N LEU C 100 O THR D 21 SHEET 15 B16 PRO C 73 GLU C 79 -1 N TYR C 77 O VAL C 98 SHEET 16 B16 MSE C 10 ILE C 24 -1 N VAL C 14 O VAL C 74 SHEET 1 C12 ALA B 96 THR B 102 0 SHEET 2 C12 VAL B 74 GLU B 79 -1 N TYR B 77 O VAL B 98 SHEET 3 C12 MSE B 10 ILE B 24 -1 N VAL B 14 O VAL B 74 SHEET 4 C12 ALA D 96 THR D 102 -1 O LEU D 100 N THR B 21 SHEET 5 C12 SER D 41 MSE D 47 1 N CYS D 45 O LEU D 97 SHEET 6 C12 LYS D 27 LYS D 35 -1 N PHE D 30 O SER D 46 SHEET 7 C12 MSE D 10 ILE D 24 -1 N HIS D 20 O CYS D 31 SHEET 8 C12 ALA C 96 THR C 102 -1 N LEU C 100 O THR D 21 SHEET 9 C12 SER C 41 MSE C 47 1 N CYS C 45 O LEU C 97 SHEET 10 C12 LYS C 27 LYS C 35 -1 N GLY C 34 O ILE C 42 SHEET 11 C12 MSE C 10 ILE C 24 -1 N HIS C 20 O CYS C 31 SHEET 12 C12 ALA A 96 THR A 102 -1 N LEU A 100 O THR C 21 SSBOND 1 CYS A 31 CYS A 45 1555 1555 2.09 SSBOND 2 CYS A 103 CYS A 109 1555 1555 2.06 SSBOND 3 CYS B 31 CYS B 45 1555 1555 2.16 SSBOND 4 CYS B 103 CYS B 109 1555 1555 2.09 SSBOND 5 CYS C 31 CYS C 45 1555 1555 2.77 SSBOND 6 CYS C 103 CYS C 109 1555 1555 2.08 SSBOND 7 CYS D 31 CYS D 45 1555 1555 2.40 SSBOND 8 CYS D 103 CYS D 109 1555 1555 2.09 SSBOND 9 CYS E 31 CYS E 45 1555 1555 2.48 SSBOND 10 CYS E 103 CYS E 109 1555 1555 2.06 LINK C GLY A 9 N MSE A 10 1555 1555 1.33 LINK C MSE A 10 N PHE A 11 1555 1555 1.32 LINK C SER A 46 N MSE A 47 1555 1555 1.32 LINK C MSE A 47 N LYS A 48 1555 1555 1.34 LINK C GLY B 9 N MSE B 10 1555 1555 1.34 LINK C MSE B 10 N PHE B 11 1555 1555 1.32 LINK C SER B 46 N MSE B 47 1555 1555 1.33 LINK C MSE B 47 N LYS B 48 1555 1555 1.33 LINK C GLY C 9 N MSE C 10 1555 1555 1.32 LINK C MSE C 10 N PHE C 11 1555 1555 1.33 LINK C SER C 46 N MSE C 47 1555 1555 1.33 LINK C MSE C 47 N LYS C 48 1555 1555 1.33 LINK C GLY D 9 N MSE D 10 1555 1555 1.34 LINK C MSE D 10 N PHE D 11 1555 1555 1.33 LINK C SER D 46 N MSE D 47 1555 1555 1.33 LINK C MSE D 47 N LYS D 48 1555 1555 1.33 LINK C GLY E 9 N MSE E 10 1555 1555 1.33 LINK C MSE E 10 N PHE E 11 1555 1555 1.34 LINK C SER E 46 N MSE E 47 1555 1555 1.33 LINK C MSE E 47 N LYS E 48 1555 1555 1.33 CISPEP 1 ASP A 8 GLY A 9 0 -13.58 CISPEP 2 ASP B 8 GLY B 9 0 -8.69 CISPEP 3 SER B 37 ALA B 38 0 -1.55 CISPEP 4 ASP C 8 GLY C 9 0 -0.05 CISPEP 5 ASP D 8 GLY D 9 0 -3.05 CISPEP 6 ASP E 8 GLY E 9 0 -11.67 CISPEP 7 GLN E 36 SER E 37 0 1.40 SITE 1 AC1 4 ASN A 62 TYR A 66 THR A 69 1PE C 127 SITE 1 AC2 5 ASN B 62 TYR B 66 HOH B 177 THR E 69 SITE 2 AC2 5 1PE E 127 SITE 1 AC3 3 1PE A 127 HOH C 204 THR D 69 SITE 1 AC4 2 TYR D 66 THR D 70 SITE 1 AC5 2 1PE B 127 ASN E 62 CRYST1 97.630 97.630 165.360 90.00 90.00 120.00 P 65 30 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 0.010243 0.005914 0.000000 0.00000 SCALE2 0.000000 0.011827 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006047 0.00000