HEADER TOXIN 03-OCT-25 9SVZ TITLE THE STRUCTURE OF S. AUREUS ALPHA-HEMOLYSIN IN COMPLEX WITH A BICYCLIC TITLE 2 PEPTIDE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-HEMOLYSIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALPHA-HL,ALPHA-TOXIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BICYCLIC PEPTIDE; COMPND 8 CHAIN: C, D; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: RESIDUE 18 (ALANINE) WAS ADDED TO INCORPORATE THE COMPND 11 AMINE ON THE C-TERMINUS OF THE BICYCLIC PEPTIDE (CONH2) AND IS NOT COMPND 12 PART OF THE BICYCLIC PEPTIDE SEQUENCE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: HLY, HLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS INHIBITOR, PORE FORMING TOXIN, A-HEMOLYSIN, BICYCLIC PEPTIDE, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR J.R.WHITESIDE,L.DIAZ-SAEZ,C.E.ROWLAND,C.G.DOWSON,N.LEWIS REVDAT 1 12-AUG-26 9SVZ 0 JRNL AUTH J.R.WHITESIDE,L.DIAZ-SAEZ,C.E.ROWLAND,C.G.DOWSON,N.LEWIS JRNL TITL THE STRUCTURE OF S. AUREUS ALPHA-HEMOLYSIN IN COMPLEX WITH A JRNL TITL 2 BICYCLIC PEPTIDE INHIBITOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0431 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 29166 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) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1522 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2129 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4760 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 84 REMARK 3 SOLVENT ATOMS : 252 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.76000 REMARK 3 B22 (A**2) : 0.23000 REMARK 3 B33 (A**2) : -0.80000 REMARK 3 B12 (A**2) : 3.44000 REMARK 3 B13 (A**2) : -1.72000 REMARK 3 B23 (A**2) : -0.70000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.307 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.221 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.173 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.774 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5003 ; 0.006 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4588 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6772 ; 1.502 ; 1.811 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10554 ; 0.530 ; 1.795 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 606 ; 7.219 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 22 ; 7.374 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 834 ;15.300 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 717 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5967 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1191 ; 0.001 ; 0.020 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): 2394 ; 2.708 ; 3.453 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2391 ; 2.699 ; 3.452 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2983 ; 4.156 ; 6.182 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2983 ; 4.156 ; 6.182 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2609 ; 3.678 ; 3.825 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2610 ; 3.678 ; 3.826 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3781 ; 5.868 ; 6.808 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5331 ; 7.791 ;38.290 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5332 ; 7.791 ;38.290 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 : 1.20 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 THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 9SVZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1292151251. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30721 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.53500 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN BUFFER:30MM HEPES PH 7.6, REMARK 280 150MM NACL AND 1MM TCEP. CRYSTALLISATION BUFFER: 0.2M CALCIUM REMARK 280 CHLORIDE DIHYDRATE, 0.1M SODIUM ACETATE AND 20% (W/V) PEG6000., REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 3 REMARK 465 SER A 4 REMARK 465 ASP A 5 REMARK 465 ILE A 6 REMARK 465 ASP A 129 REMARK 465 THR A 130 REMARK 465 GLY A 131 REMARK 465 LYS A 132 REMARK 465 ILE A 133 REMARK 465 GLY A 134 REMARK 465 GLY A 135 REMARK 465 LEU A 136 REMARK 465 ILE A 137 REMARK 465 GLY A 138 REMARK 465 ALA A 139 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ASP B 3 REMARK 465 SER B 4 REMARK 465 ASP B 5 REMARK 465 ILE B 6 REMARK 465 THR B 130 REMARK 465 GLY B 131 REMARK 465 LYS B 132 REMARK 465 ILE B 133 REMARK 465 GLY B 134 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 31 CG CD CE NZ REMARK 470 LYS A 238 CG CD CE NZ REMARK 470 LYS B 76 CD CE NZ REMARK 470 ALA C 18 CA C O CB REMARK 470 ALA D 18 CA C O CB REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 165 CD CE REMARK 480 LYS B 9 CD CE NZ REMARK 480 LYS B 111 CE NZ REMARK 480 LYS B 165 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 NZ LYS B 165 O HOH B 401 1.82 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 165 CE LYS A 165 NZ -0.269 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 B 252 NE - CZ - NH1 ANGL. DEV. = 3.0 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 LYS A 59 -161.85 -124.86 REMARK 500 GLN A 65 24.85 80.16 REMARK 500 TYR A 66 109.44 -41.12 REMARK 500 ASN A 122 19.74 -146.47 REMARK 500 GLN A 151 49.74 -146.17 REMARK 500 ASP A 153 -2.68 79.46 REMARK 500 ASN A 173 -85.08 -108.47 REMARK 500 SER A 187 133.32 -39.68 REMARK 500 ASN A 202 17.21 -140.84 REMARK 500 SER A 222 -74.50 -110.40 REMARK 500 ASP A 228 83.18 -151.12 REMARK 500 SER A 263 -28.18 122.12 REMARK 500 ILE B 15 32.32 -99.30 REMARK 500 LYS B 59 -161.05 -128.67 REMARK 500 GLN B 65 30.10 74.40 REMARK 500 PHE B 121 42.49 36.10 REMARK 500 ASN B 122 20.25 -145.30 REMARK 500 LEU B 136 134.60 173.55 REMARK 500 GLN B 151 53.12 -151.10 REMARK 500 ASP B 153 -0.40 83.78 REMARK 500 SER B 160 60.70 24.26 REMARK 500 ASN B 173 -78.20 -102.09 REMARK 500 GLN B 178 64.42 35.84 REMARK 500 ASN B 202 31.85 -153.73 REMARK 500 MET B 205 -178.21 -65.60 REMARK 500 SER B 222 -75.36 -105.63 REMARK 500 ASP B 228 81.86 -153.75 REMARK 500 GLN B 242 45.32 -105.17 REMARK 500 SER B 263 -27.14 121.45 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 185 0.10 SIDE CHAIN REMARK 500 ARG B 237 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 521 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A 522 DISTANCE = 7.89 ANGSTROMS REMARK 525 HOH C 508 DISTANCE = 6.09 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 101 OD2 REMARK 620 2 ASN A 124 OD1 163.4 REMARK 620 3 VAL A 125 O 81.9 81.6 REMARK 620 4 ACT A 303 O 93.3 98.8 129.1 REMARK 620 5 ACT A 303 OXT 98.7 79.8 77.1 53.5 REMARK 620 6 HOH A 406 O 85.5 87.1 71.4 159.1 147.3 REMARK 620 7 HOH B 427 O 88.3 106.7 160.1 68.5 121.8 90.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 101 OD2 REMARK 620 2 ASN B 124 OD1 165.0 REMARK 620 3 VAL B 125 O 81.0 84.2 REMARK 620 4 ACT B 302 OXT 92.6 83.1 79.4 REMARK 620 5 HOH B 424 O 94.5 99.0 159.9 81.2 REMARK 620 6 HOH B 429 O 109.0 68.4 75.4 143.3 124.4 REMARK 620 7 HOH B 441 O 101.9 88.9 130.0 148.6 70.1 56.3 REMARK 620 N 1 2 3 4 5 6 DBREF 9SVZ A 2 294 UNP P09616 HLA_STAAU 27 319 DBREF 9SVZ B 2 294 UNP P09616 HLA_STAAU 27 319 DBREF 9SVZ C 1 18 PDB 9SVZ 9SVZ 1 18 DBREF 9SVZ D 1 18 PDB 9SVZ 9SVZ 1 18 SEQADV 9SVZ MET A 1 UNP P09616 INITIATING METHIONINE SEQADV 9SVZ ALA A 36 UNP P09616 HIS 61 CONFLICT SEQADV 9SVZ MET B 1 UNP P09616 INITIATING METHIONINE SEQADV 9SVZ ALA B 36 UNP P09616 HIS 61 CONFLICT SEQRES 1 A 294 MET ALA ASP SER ASP ILE ASN ILE LYS THR GLY THR THR SEQRES 2 A 294 ASP ILE GLY SER ASN THR THR VAL LYS THR GLY ASP LEU SEQRES 3 A 294 VAL THR TYR ASP LYS GLU ASN GLY MET ALA LYS LYS VAL SEQRES 4 A 294 PHE TYR SER PHE ILE ASP ASP LYS ASN HIS ASN LYS LYS SEQRES 5 A 294 LEU LEU VAL ILE ARG THR LYS GLY THR ILE ALA GLY GLN SEQRES 6 A 294 TYR ARG VAL TYR SER GLU GLU GLY ALA ASN LYS SER GLY SEQRES 7 A 294 LEU ALA TRP PRO SER ALA PHE LYS VAL GLN LEU GLN LEU SEQRES 8 A 294 PRO ASP ASN GLU VAL ALA GLN ILE SER ASP TYR TYR PRO SEQRES 9 A 294 ARG ASN SER ILE ASP THR LYS GLU TYR MET SER THR LEU SEQRES 10 A 294 THR TYR GLY PHE ASN GLY ASN VAL THR GLY ASP ASP THR SEQRES 11 A 294 GLY LYS ILE GLY GLY LEU ILE GLY ALA ASN VAL SER ILE SEQRES 12 A 294 GLY HIS THR LEU LYS TYR VAL GLN PRO ASP PHE LYS THR SEQRES 13 A 294 ILE LEU GLU SER PRO THR ASP LYS LYS VAL GLY TRP LYS SEQRES 14 A 294 VAL ILE PHE ASN ASN MET VAL ASN GLN ASN TRP GLY PRO SEQRES 15 A 294 TYR ASP ARG ASP SER TRP ASN PRO VAL TYR GLY ASN GLN SEQRES 16 A 294 LEU PHE MET LYS THR ARG ASN GLY SER MET LYS ALA ALA SEQRES 17 A 294 ASP ASN PHE LEU ASP PRO ASN LYS ALA SER SER LEU LEU SEQRES 18 A 294 SER SER GLY PHE SER PRO ASP PHE ALA THR VAL ILE THR SEQRES 19 A 294 MET ASP ARG LYS ALA SER LYS GLN GLN THR ASN ILE ASP SEQRES 20 A 294 VAL ILE TYR GLU ARG VAL ARG ASP ASP TYR GLN LEU HIS SEQRES 21 A 294 TRP THR SER THR ASN TRP LYS GLY THR ASN THR LYS ASP SEQRES 22 A 294 LYS TRP THR ASP ARG SER SER GLU ARG TYR LYS ILE ASP SEQRES 23 A 294 TRP GLU LYS GLU GLU MET THR ASN SEQRES 1 B 294 MET ALA ASP SER ASP ILE ASN ILE LYS THR GLY THR THR SEQRES 2 B 294 ASP ILE GLY SER ASN THR THR VAL LYS THR GLY ASP LEU SEQRES 3 B 294 VAL THR TYR ASP LYS GLU ASN GLY MET ALA LYS LYS VAL SEQRES 4 B 294 PHE TYR SER PHE ILE ASP ASP LYS ASN HIS ASN LYS LYS SEQRES 5 B 294 LEU LEU VAL ILE ARG THR LYS GLY THR ILE ALA GLY GLN SEQRES 6 B 294 TYR ARG VAL TYR SER GLU GLU GLY ALA ASN LYS SER GLY SEQRES 7 B 294 LEU ALA TRP PRO SER ALA PHE LYS VAL GLN LEU GLN LEU SEQRES 8 B 294 PRO ASP ASN GLU VAL ALA GLN ILE SER ASP TYR TYR PRO SEQRES 9 B 294 ARG ASN SER ILE ASP THR LYS GLU TYR MET SER THR LEU SEQRES 10 B 294 THR TYR GLY PHE ASN GLY ASN VAL THR GLY ASP ASP THR SEQRES 11 B 294 GLY LYS ILE GLY GLY LEU ILE GLY ALA ASN VAL SER ILE SEQRES 12 B 294 GLY HIS THR LEU LYS TYR VAL GLN PRO ASP PHE LYS THR SEQRES 13 B 294 ILE LEU GLU SER PRO THR ASP LYS LYS VAL GLY TRP LYS SEQRES 14 B 294 VAL ILE PHE ASN ASN MET VAL ASN GLN ASN TRP GLY PRO SEQRES 15 B 294 TYR ASP ARG ASP SER TRP ASN PRO VAL TYR GLY ASN GLN SEQRES 16 B 294 LEU PHE MET LYS THR ARG ASN GLY SER MET LYS ALA ALA SEQRES 17 B 294 ASP ASN PHE LEU ASP PRO ASN LYS ALA SER SER LEU LEU SEQRES 18 B 294 SER SER GLY PHE SER PRO ASP PHE ALA THR VAL ILE THR SEQRES 19 B 294 MET ASP ARG LYS ALA SER LYS GLN GLN THR ASN ILE ASP SEQRES 20 B 294 VAL ILE TYR GLU ARG VAL ARG ASP ASP TYR GLN LEU HIS SEQRES 21 B 294 TRP THR SER THR ASN TRP LYS GLY THR ASN THR LYS ASP SEQRES 22 B 294 LYS TRP THR ASP ARG SER SER GLU ARG TYR LYS ILE ASP SEQRES 23 B 294 TRP GLU LYS GLU GLU MET THR ASN SEQRES 1 C 18 ALA CYS PRO THR LEU ASN TYR CYS TRP ASN PRO PHE MET SEQRES 2 C 18 SER VAL CYS ALA ALA SEQRES 1 D 18 ALA CYS PRO THR LEU ASN TYR CYS TRP ASN PRO PHE MET SEQRES 2 D 18 SER VAL CYS ALA ALA HET MG A 301 1 HET ACT A 302 4 HET ACT A 303 4 HET EDO A 304 4 HET EDO A 305 4 HET EDO A 306 4 HET ACT A 307 4 HET EDO A 308 4 HET MG B 301 1 HET ACT B 302 4 HET EDO B 303 4 HET EDO B 304 4 HET GOL B 305 6 HET EDO B 306 4 HET R06 C 401 15 HET CL C 402 1 HET R06 D 101 15 HET CL D 102 1 HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETNAM R06 1-[3,5-BIS(2-CHLORANYLETHANOYL)-1,3,5-TRIAZINAN-1-YL]- HETNAM 2 R06 2-CHLORANYL-ETHANONE HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 MG 2(MG 2+) FORMUL 6 ACT 4(C2 H3 O2 1-) FORMUL 8 EDO 7(C2 H6 O2) FORMUL 17 GOL C3 H8 O3 FORMUL 19 R06 2(C9 H12 CL3 N3 O3) FORMUL 20 CL 2(CL 1-) FORMUL 23 HOH *252(H2 O) HELIX 1 AA1 LYS A 206 ASN A 210 5 5 HELIX 2 AA2 ASP A 213 ALA A 217 5 5 HELIX 3 AA3 SER A 218 SER A 222 5 5 HELIX 4 AA4 LYS B 206 ASN B 210 5 5 HELIX 5 AA5 ASP B 213 ALA B 217 5 5 HELIX 6 AA6 SER B 218 SER B 222 5 5 HELIX 7 AA7 MET C 13 ALA C 17 5 5 HELIX 8 AA8 MET D 13 ALA D 17 5 5 SHEET 1 AA1 6 GLY A 11 GLY A 16 0 SHEET 2 AA1 6 THR A 19 ASP A 30 -1 O THR A 23 N GLY A 11 SHEET 3 AA1 6 MET A 35 ASP A 46 -1 O MET A 35 N ASP A 30 SHEET 4 AA1 6 LYS A 51 ILE A 62 -1 O ARG A 57 N PHE A 40 SHEET 5 AA1 6 PHE A 229 ASP A 236 -1 O THR A 231 N ILE A 56 SHEET 6 AA1 6 GLN A 98 TYR A 103 -1 N SER A 100 O VAL A 232 SHEET 1 AA2 4 ARG A 67 GLU A 72 0 SHEET 2 AA2 4 LYS A 76 GLN A 90 -1 O ALA A 80 N ARG A 67 SHEET 3 AA2 4 LYS A 165 PHE A 172 -1 O VAL A 170 N PHE A 85 SHEET 4 AA2 4 PHE A 154 LEU A 158 -1 N ILE A 157 O LYS A 169 SHEET 1 AA3 5 ARG A 67 GLU A 72 0 SHEET 2 AA3 5 LYS A 76 GLN A 90 -1 O ALA A 80 N ARG A 67 SHEET 3 AA3 5 GLN A 243 TRP A 261 -1 O TYR A 257 N LEU A 79 SHEET 4 AA3 5 TRP A 266 ASP A 286 -1 O ILE A 285 N THR A 244 SHEET 5 AA3 5 GLU A 291 THR A 293 -1 O GLU A 291 N ASP A 286 SHEET 1 AA4 3 VAL A 125 ASP A 128 0 SHEET 2 AA4 3 GLU A 112 TYR A 119 -1 N THR A 118 O THR A 126 SHEET 3 AA4 3 VAL A 141 VAL A 150 -1 O TYR A 149 N TYR A 113 SHEET 1 AA5 2 MET A 175 ASN A 177 0 SHEET 2 AA5 2 TRP A 180 TYR A 183 -1 O TRP A 180 N ASN A 177 SHEET 1 AA6 6 GLY B 11 ASP B 14 0 SHEET 2 AA6 6 THR B 19 ASP B 30 -1 O THR B 23 N GLY B 11 SHEET 3 AA6 6 MET B 35 ASP B 46 -1 O MET B 35 N ASP B 30 SHEET 4 AA6 6 LYS B 51 ILE B 62 -1 O ARG B 57 N PHE B 40 SHEET 5 AA6 6 PHE B 229 ASP B 236 -1 O PHE B 229 N THR B 58 SHEET 6 AA6 6 GLN B 98 TYR B 103 -1 N GLN B 98 O THR B 234 SHEET 1 AA7 4 ARG B 67 GLU B 72 0 SHEET 2 AA7 4 LYS B 76 GLN B 90 -1 O ALA B 80 N ARG B 67 SHEET 3 AA7 4 LYS B 165 PHE B 172 -1 O PHE B 172 N SER B 83 SHEET 4 AA7 4 PHE B 154 GLU B 159 -1 N GLU B 159 O GLY B 167 SHEET 1 AA8 5 ARG B 67 GLU B 72 0 SHEET 2 AA8 5 LYS B 76 GLN B 90 -1 O ALA B 80 N ARG B 67 SHEET 3 AA8 5 GLN B 243 TRP B 261 -1 O ASP B 255 N TRP B 81 SHEET 4 AA8 5 TRP B 266 ASP B 286 -1 O TRP B 275 N ARG B 254 SHEET 5 AA8 5 GLU B 291 THR B 293 -1 O THR B 293 N LYS B 284 SHEET 1 AA9 3 VAL B 125 ASP B 128 0 SHEET 2 AA9 3 GLU B 112 TYR B 119 -1 N THR B 116 O ASP B 128 SHEET 3 AA9 3 VAL B 141 VAL B 150 -1 O VAL B 141 N TYR B 119 SHEET 1 AB1 2 MET B 175 VAL B 176 0 SHEET 2 AB1 2 PRO B 182 TYR B 183 -1 O TYR B 183 N MET B 175 LINK SG CYS C 2 C5 R06 C 401 1555 1555 1.85 LINK SG CYS C 8 C1 R06 C 401 1555 1555 1.78 LINK SG CYS C 16 C8 R06 C 401 1555 1555 1.80 LINK SG CYS D 2 C5 R06 D 101 1555 1555 1.84 LINK SG CYS D 8 C8 R06 D 101 1555 1555 1.79 LINK SG CYS D 16 C1 R06 D 101 1555 1555 1.77 LINK OD2 ASP A 101 MG MG A 301 1555 1555 2.35 LINK OD1 ASN A 124 MG MG A 301 1555 1555 2.24 LINK O VAL A 125 MG MG A 301 1555 1555 2.31 LINK MG MG A 301 O ACT A 303 1555 1555 2.62 LINK MG MG A 301 OXT ACT A 303 1555 1555 2.14 LINK MG MG A 301 O HOH A 406 1555 1555 1.99 LINK MG MG A 301 O HOH B 427 1555 1555 2.34 LINK OD2 ASP B 101 MG MG B 301 1555 1555 2.37 LINK OD1 ASN B 124 MG MG B 301 1555 1555 2.44 LINK O VAL B 125 MG MG B 301 1555 1555 2.37 LINK MG MG B 301 OXT ACT B 302 1555 1555 2.33 LINK MG MG B 301 O HOH B 424 1555 1555 2.20 LINK MG MG B 301 O HOH B 429 1555 1555 2.36 LINK MG MG B 301 O HOH B 441 1555 1555 2.67 CISPEP 1 TYR A 103 PRO A 104 0 3.01 CISPEP 2 GLY A 181 PRO A 182 0 5.82 CISPEP 3 TYR B 103 PRO B 104 0 -10.45 CRYST1 53.839 59.041 72.473 71.15 86.36 70.58 P 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 0.018574 -0.006547 0.000972 0.00000 SCALE2 0.000000 0.017959 -0.006084 0.00000 SCALE3 0.000000 0.000000 0.014598 0.00000 CONECT 734 4824 CONECT 933 4824 CONECT 938 4824 CONECT 3012 4853 CONECT 3208 4853 CONECT 3213 4853 CONECT 4563 4882 CONECT 4616 4876 CONECT 4683 4887 CONECT 4701 4898 CONECT 4749 4903 CONECT 4816 4892 CONECT 4824 734 933 938 4830 CONECT 4824 4831 4913 5056 CONECT 4825 4826 4827 4828 CONECT 4826 4825 CONECT 4827 4825 CONECT 4828 4825 CONECT 4829 4830 4831 4832 CONECT 4830 4824 4829 CONECT 4831 4824 4829 CONECT 4832 4829 CONECT 4833 4834 4835 CONECT 4834 4833 CONECT 4835 4833 4836 CONECT 4836 4835 CONECT 4837 4838 4839 CONECT 4838 4837 CONECT 4839 4837 4840 CONECT 4840 4839 CONECT 4841 4842 4843 CONECT 4842 4841 CONECT 4843 4841 4844 CONECT 4844 4843 CONECT 4845 4846 4847 4848 CONECT 4846 4845 CONECT 4847 4845 CONECT 4848 4845 CONECT 4849 4850 4851 CONECT 4850 4849 CONECT 4851 4849 4852 CONECT 4852 4851 CONECT 4853 3012 3208 3213 4856 CONECT 4853 5053 5058 5070 CONECT 4854 4855 4856 4857 CONECT 4855 4854 CONECT 4856 4853 4854 CONECT 4857 4854 CONECT 4858 4859 4860 CONECT 4859 4858 CONECT 4860 4858 4861 CONECT 4861 4860 CONECT 4862 4863 4864 CONECT 4863 4862 CONECT 4864 4862 4865 CONECT 4865 4864 CONECT 4866 4867 4868 CONECT 4867 4866 CONECT 4868 4866 4869 4870 CONECT 4869 4868 CONECT 4870 4868 4871 CONECT 4871 4870 CONECT 4872 4873 4874 CONECT 4873 4872 CONECT 4874 4872 4875 CONECT 4875 4874 CONECT 4876 4616 4877 CONECT 4877 4876 4878 4890 CONECT 4878 4877 4879 4889 CONECT 4879 4878 4880 CONECT 4880 4879 4881 4884 CONECT 4881 4880 4882 4883 CONECT 4882 4563 4881 CONECT 4883 4881 CONECT 4884 4880 4885 CONECT 4885 4884 4886 4889 CONECT 4886 4885 4887 4888 CONECT 4887 4683 4886 CONECT 4888 4886 CONECT 4889 4878 4885 CONECT 4890 4877 CONECT 4892 4816 4893 CONECT 4893 4892 4894 4906 CONECT 4894 4893 4895 4905 CONECT 4895 4894 4896 CONECT 4896 4895 4897 4900 CONECT 4897 4896 4898 4899 CONECT 4898 4701 4897 CONECT 4899 4897 CONECT 4900 4896 4901 CONECT 4901 4900 4902 4905 CONECT 4902 4901 4903 4904 CONECT 4903 4749 4902 CONECT 4904 4902 CONECT 4905 4894 4901 CONECT 4906 4893 CONECT 4913 4824 CONECT 5053 4853 CONECT 5056 4824 CONECT 5058 4853 CONECT 5070 4853 MASTER 435 0 18 8 40 0 0 6 5096 4 101 50 END