HEADER HYDROLASE/HYDROLASE INHIBITOR 04-OCT-19 6UKD TITLE CO-COMPLEX OF S. PYOGENES 10782 STREPTOPAIN BOUND WITH A NITRILE-BASED TITLE 2 SPECIFIC COVALENT INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: STREPTOPAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 28-398; COMPND 5 SYNONYM: EXOTOXIN TYPE B,SPE B,STREPTOCOCCAL CYSTEINE PROTEINASE, COMPND 6 STREPTOCOCCUS PEPTIDASE A,SPP; COMPND 7 EC: 3.4.22.10; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES ATCC 10782; SOURCE 3 ORGANISM_TAXID: 864568; SOURCE 4 GENE: SPEB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET23B KEYWDS SPEB, STREPTOPAIN, INHIBITOR, NITRILE, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.W.WOLAN,J.L.WOEHL,S.KITAMURA REVDAT 2 11-OCT-23 6UKD 1 REMARK REVDAT 1 09-SEP-20 6UKD 0 JRNL AUTH J.L.WOEHL,S.KITAMURA,N.DILLON,Z.HAN,L.J.EDGAR,V.NIZET, JRNL AUTH 2 D.W.WOLAN JRNL TITL AN IRREVERSIBLE INHIBITOR TO PROBE THE ROLE OFSTREPTOCOCCUS JRNL TITL 2 PYOGENESCYSTEINE PROTEASE SPEB IN EVASION OF HOST COMPLEMENT JRNL TITL 3 DEFENSES. JRNL REF ACS CHEM.BIOL. V. 15 2060 2020 JRNL REFN ESSN 1554-8937 JRNL PMID 32662975 JRNL DOI 10.1021/ACSCHEMBIO.0C00191 REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 29406 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 1408 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 1.6500 - 1.5900 0.00 0 0 0.2070 0.2570 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 146 THROUGH 204 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.6601 -11.3671 20.7099 REMARK 3 T TENSOR REMARK 3 T11: 0.0714 T22: 0.0748 REMARK 3 T33: 0.0545 T12: -0.0125 REMARK 3 T13: 0.0012 T23: -0.0043 REMARK 3 L TENSOR REMARK 3 L11: 0.7137 L22: 0.2505 REMARK 3 L33: 0.4186 L12: 0.1411 REMARK 3 L13: -0.0283 L23: 0.0743 REMARK 3 S TENSOR REMARK 3 S11: -0.0243 S12: -0.0378 S13: -0.0114 REMARK 3 S21: 0.0302 S22: 0.0748 S23: 0.0198 REMARK 3 S31: 0.0268 S32: -0.0400 S33: 0.0117 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 205 THROUGH 254 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.9312 -4.6561 13.3729 REMARK 3 T TENSOR REMARK 3 T11: 0.0710 T22: 0.0654 REMARK 3 T33: 0.0863 T12: -0.0230 REMARK 3 T13: 0.0123 T23: -0.0148 REMARK 3 L TENSOR REMARK 3 L11: 0.2505 L22: 0.5957 REMARK 3 L33: 0.9099 L12: -0.1512 REMARK 3 L13: -0.1734 L23: -0.0244 REMARK 3 S TENSOR REMARK 3 S11: 0.0086 S12: 0.0165 S13: 0.0101 REMARK 3 S21: -0.0275 S22: 0.0190 S23: -0.0004 REMARK 3 S31: -0.0641 S32: 0.0807 S33: -0.0004 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 255 THROUGH 272 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.3766 -5.5440 17.9642 REMARK 3 T TENSOR REMARK 3 T11: 0.0897 T22: 0.0703 REMARK 3 T33: 0.0875 T12: -0.0054 REMARK 3 T13: 0.0032 T23: -0.0031 REMARK 3 L TENSOR REMARK 3 L11: 0.9521 L22: 0.2670 REMARK 3 L33: 0.0934 L12: -0.2739 REMARK 3 L13: 0.0767 L23: -0.1499 REMARK 3 S TENSOR REMARK 3 S11: 0.0322 S12: -0.0511 S13: 0.0032 REMARK 3 S21: 0.0268 S22: 0.0814 S23: -0.1276 REMARK 3 S31: -0.0103 S32: 0.0529 S33: -0.0224 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 273 THROUGH 356 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.9413 -23.7058 10.9405 REMARK 3 T TENSOR REMARK 3 T11: 0.0609 T22: 0.0506 REMARK 3 T33: 0.0508 T12: -0.0052 REMARK 3 T13: 0.0015 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.6617 L22: 0.9003 REMARK 3 L33: 0.6599 L12: 0.2779 REMARK 3 L13: -0.1481 L23: 0.1335 REMARK 3 S TENSOR REMARK 3 S11: -0.0174 S12: 0.0159 S13: -0.0929 REMARK 3 S21: -0.0449 S22: 0.0367 S23: -0.0023 REMARK 3 S31: 0.0668 S32: -0.0198 S33: 0.0257 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 357 THROUGH 402 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.1963 -24.6276 17.9578 REMARK 3 T TENSOR REMARK 3 T11: 0.0759 T22: 0.0564 REMARK 3 T33: 0.0659 T12: 0.0007 REMARK 3 T13: 0.0052 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.4476 L22: 0.9984 REMARK 3 L33: 1.0104 L12: 0.3647 REMARK 3 L13: 0.4483 L23: 0.0874 REMARK 3 S TENSOR REMARK 3 S11: 0.0060 S12: -0.0177 S13: 0.0470 REMARK 3 S21: 0.0479 S22: 0.0646 S23: 0.0201 REMARK 3 S31: 0.0422 S32: -0.1058 S33: 0.0122 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6UKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1000244769. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97945 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29409 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 46.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.40400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: PDB ENTRY 4D8B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM NITRATE, 33% PEG3350, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.19900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.24850 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.19900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 57.24850 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 KCAL/MOL 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 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 A 771 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 841 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 854 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 908 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 MET A 27 REMARK 465 ASP A 28 REMARK 465 GLN A 29 REMARK 465 ASN A 30 REMARK 465 PHE A 31 REMARK 465 ALA A 32 REMARK 465 ARG A 33 REMARK 465 ASN A 34 REMARK 465 GLU A 35 REMARK 465 LYS A 36 REMARK 465 GLU A 37 REMARK 465 ALA A 38 REMARK 465 LYS A 39 REMARK 465 ASP A 40 REMARK 465 SER A 41 REMARK 465 ALA A 42 REMARK 465 ILE A 43 REMARK 465 THR A 44 REMARK 465 PHE A 45 REMARK 465 ILE A 46 REMARK 465 GLN A 47 REMARK 465 LYS A 48 REMARK 465 SER A 49 REMARK 465 ALA A 50 REMARK 465 ALA A 51 REMARK 465 ILE A 52 REMARK 465 LYS A 53 REMARK 465 ALA A 54 REMARK 465 GLY A 55 REMARK 465 ALA A 56 REMARK 465 ARG A 57 REMARK 465 SER A 58 REMARK 465 ALA A 59 REMARK 465 GLU A 60 REMARK 465 ASP A 61 REMARK 465 ILE A 62 REMARK 465 LYS A 63 REMARK 465 LEU A 64 REMARK 465 ASP A 65 REMARK 465 LYS A 66 REMARK 465 VAL A 67 REMARK 465 ASN A 68 REMARK 465 LEU A 69 REMARK 465 GLY A 70 REMARK 465 GLY A 71 REMARK 465 GLU A 72 REMARK 465 LEU A 73 REMARK 465 SER A 74 REMARK 465 GLY A 75 REMARK 465 SER A 76 REMARK 465 ASN A 77 REMARK 465 MET A 78 REMARK 465 TYR A 79 REMARK 465 VAL A 80 REMARK 465 TYR A 81 REMARK 465 ASN A 82 REMARK 465 ILE A 83 REMARK 465 SER A 84 REMARK 465 THR A 85 REMARK 465 GLY A 86 REMARK 465 GLY A 87 REMARK 465 PHE A 88 REMARK 465 VAL A 89 REMARK 465 ILE A 90 REMARK 465 VAL A 91 REMARK 465 SER A 92 REMARK 465 GLY A 93 REMARK 465 ASP A 94 REMARK 465 LYS A 95 REMARK 465 ARG A 96 REMARK 465 SER A 97 REMARK 465 PRO A 98 REMARK 465 GLU A 99 REMARK 465 ILE A 100 REMARK 465 LEU A 101 REMARK 465 GLY A 102 REMARK 465 TYR A 103 REMARK 465 SER A 104 REMARK 465 THR A 105 REMARK 465 SER A 106 REMARK 465 GLY A 107 REMARK 465 SER A 108 REMARK 465 PHE A 109 REMARK 465 ASP A 110 REMARK 465 ALA A 111 REMARK 465 ASN A 112 REMARK 465 GLY A 113 REMARK 465 LYS A 114 REMARK 465 GLU A 115 REMARK 465 ASN A 116 REMARK 465 ILE A 117 REMARK 465 ALA A 118 REMARK 465 SER A 119 REMARK 465 PHE A 120 REMARK 465 MET A 121 REMARK 465 GLU A 122 REMARK 465 SER A 123 REMARK 465 TYR A 124 REMARK 465 VAL A 125 REMARK 465 GLU A 126 REMARK 465 GLN A 127 REMARK 465 ILE A 128 REMARK 465 LYS A 129 REMARK 465 GLU A 130 REMARK 465 ASN A 131 REMARK 465 LYS A 132 REMARK 465 LYS A 133 REMARK 465 LEU A 134 REMARK 465 ASP A 135 REMARK 465 THR A 136 REMARK 465 THR A 137 REMARK 465 TYR A 138 REMARK 465 ALA A 139 REMARK 465 GLY A 140 REMARK 465 THR A 141 REMARK 465 ALA A 142 REMARK 465 GLU A 143 REMARK 465 ILE A 144 REMARK 465 LYS A 145 REMARK 465 HIS A 403 REMARK 465 HIS A 404 REMARK 465 HIS A 405 REMARK 465 HIS A 406 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 321 CG CD CE NZ REMARK 470 GLU A 400 CG CD OE1 OE2 REMARK 470 HIS A 402 CG ND1 CD2 CE1 NE2 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 NH1 ARG A 252 O ASP A 370 3455 1.85 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 ASP A 345 18.74 -141.12 REMARK 500 SER A 363 -4.78 71.98 REMARK 500 ALA A 371 56.68 -145.54 REMARK 500 PHE A 386 63.21 -105.18 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 916 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A 917 DISTANCE = 8.24 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue Q9D A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 503 DBREF 6UKD A 28 398 UNP P0C0J0 SPEB_STRPY 28 398 SEQADV 6UKD MET A 27 UNP P0C0J0 INITIATING METHIONINE SEQADV 6UKD ASN A 154 UNP P0C0J0 ASP 154 VARIANT SEQADV 6UKD LEU A 399 UNP P0C0J0 EXPRESSION TAG SEQADV 6UKD GLU A 400 UNP P0C0J0 EXPRESSION TAG SEQADV 6UKD HIS A 401 UNP P0C0J0 EXPRESSION TAG SEQADV 6UKD HIS A 402 UNP P0C0J0 EXPRESSION TAG SEQADV 6UKD HIS A 403 UNP P0C0J0 EXPRESSION TAG SEQADV 6UKD HIS A 404 UNP P0C0J0 EXPRESSION TAG SEQADV 6UKD HIS A 405 UNP P0C0J0 EXPRESSION TAG SEQADV 6UKD HIS A 406 UNP P0C0J0 EXPRESSION TAG SEQRES 1 A 380 MET ASP GLN ASN PHE ALA ARG ASN GLU LYS GLU ALA LYS SEQRES 2 A 380 ASP SER ALA ILE THR PHE ILE GLN LYS SER ALA ALA ILE SEQRES 3 A 380 LYS ALA GLY ALA ARG SER ALA GLU ASP ILE LYS LEU ASP SEQRES 4 A 380 LYS VAL ASN LEU GLY GLY GLU LEU SER GLY SER ASN MET SEQRES 5 A 380 TYR VAL TYR ASN ILE SER THR GLY GLY PHE VAL ILE VAL SEQRES 6 A 380 SER GLY ASP LYS ARG SER PRO GLU ILE LEU GLY TYR SER SEQRES 7 A 380 THR SER GLY SER PHE ASP ALA ASN GLY LYS GLU ASN ILE SEQRES 8 A 380 ALA SER PHE MET GLU SER TYR VAL GLU GLN ILE LYS GLU SEQRES 9 A 380 ASN LYS LYS LEU ASP THR THR TYR ALA GLY THR ALA GLU SEQRES 10 A 380 ILE LYS GLN PRO VAL VAL LYS SER LEU LEU ASN SER LYS SEQRES 11 A 380 GLY ILE HIS TYR ASN GLN GLY ASN PRO TYR ASN LEU LEU SEQRES 12 A 380 THR PRO VAL ILE GLU LYS VAL LYS PRO GLY GLU GLN SER SEQRES 13 A 380 PHE VAL GLY GLN HIS ALA ALA THR GLY CYS VAL ALA THR SEQRES 14 A 380 ALA THR ALA GLN ILE MET LYS TYR HIS ASN TYR PRO ASN SEQRES 15 A 380 LYS GLY LEU LYS ASP TYR THR TYR THR LEU SER SER ASN SEQRES 16 A 380 ASN PRO TYR PHE ASN HIS PRO LYS ASN LEU PHE ALA ALA SEQRES 17 A 380 ILE SER THR ARG GLN TYR ASN TRP ASN ASN ILE LEU PRO SEQRES 18 A 380 THR TYR SER GLY ARG GLU SER ASN VAL GLN LYS MET ALA SEQRES 19 A 380 ILE SER GLU LEU MET ALA ASP VAL GLY ILE SER VAL ASP SEQRES 20 A 380 MET ASP TYR GLY PRO SER SER GLY SER ALA GLY SER SER SEQRES 21 A 380 ARG VAL GLN ARG ALA LEU LYS GLU ASN PHE GLY TYR ASN SEQRES 22 A 380 GLN SER VAL HIS GLN ILE ASN ARG SER ASP PHE SER LYS SEQRES 23 A 380 GLN ASP TRP GLU ALA GLN ILE ASP LYS GLU LEU SER GLN SEQRES 24 A 380 ASN GLN PRO VAL TYR TYR GLN GLY VAL GLY LYS VAL GLY SEQRES 25 A 380 GLY HIS ALA PHE VAL ILE ASP GLY ALA ASP GLY ARG ASN SEQRES 26 A 380 PHE TYR HIS VAL ASN TRP GLY TRP GLY GLY VAL SER ASP SEQRES 27 A 380 GLY PHE PHE ARG LEU ASP ALA LEU ASN PRO SER ALA LEU SEQRES 28 A 380 GLY THR GLY GLY GLY ALA GLY GLY PHE ASN GLY TYR GLN SEQRES 29 A 380 SER ALA VAL VAL GLY ILE LYS PRO LEU GLU HIS HIS HIS SEQRES 30 A 380 HIS HIS HIS HET Q9D A 501 25 HET NO3 A 502 4 HET NO3 A 503 4 HETNAM Q9D BENZYL [(2S)-1-(3-NITROPHENYL)-3-OXOBUTAN-2- HETNAM 2 Q9D YL]CARBAMATE HETNAM NO3 NITRATE ION FORMUL 2 Q9D C18 H18 N2 O5 FORMUL 3 NO3 2(N O3 1-) FORMUL 5 HOH *317(H2 O) HELIX 1 AA1 SER A 151 LYS A 156 1 6 HELIX 2 AA2 GLY A 191 ASN A 205 1 15 HELIX 3 AA3 ALA A 234 ARG A 238 5 5 HELIX 4 AA4 SER A 254 VAL A 272 1 19 HELIX 5 AA5 GLY A 284 ASN A 295 1 12 HELIX 6 AA6 SER A 308 PHE A 310 5 3 HELIX 7 AA7 SER A 311 GLN A 325 1 15 SHEET 1 AA1 5 VAL A 148 VAL A 149 0 SHEET 2 AA1 5 GLY A 338 ASP A 348 -1 O ALA A 347 N VAL A 149 SHEET 3 AA1 5 VAL A 329 GLY A 335 -1 N TYR A 331 O PHE A 342 SHEET 4 AA1 5 GLY A 388 VAL A 394 -1 O GLY A 388 N VAL A 334 SHEET 5 AA1 5 HIS A 303 ASN A 306 -1 N ILE A 305 O ALA A 392 SHEET 1 AA2 4 VAL A 148 VAL A 149 0 SHEET 2 AA2 4 GLY A 338 ASP A 348 -1 O ALA A 347 N VAL A 149 SHEET 3 AA2 4 TYR A 353 ASN A 356 -1 O ASN A 356 N VAL A 343 SHEET 4 AA2 4 GLY A 365 PHE A 367 -1 O PHE A 367 N TYR A 353 SHEET 1 AA3 2 TYR A 214 THR A 217 0 SHEET 2 AA3 2 ASN A 230 ALA A 233 -1 O LEU A 231 N TYR A 216 LINK SG CYS A 192 C56 Q9D A 501 1555 1555 1.93 CISPEP 1 ASN A 164 PRO A 165 0 -1.14 CISPEP 2 TYR A 206 PRO A 207 0 4.19 CISPEP 3 HIS A 227 PRO A 228 0 -3.50 SITE 1 AC1 16 GLN A 162 CYS A 192 VAL A 193 ASN A 208 SITE 2 AC1 16 SER A 280 GLY A 281 SER A 282 ALA A 283 SITE 3 AC1 16 GLN A 332 GLY A 333 VAL A 334 GLY A 339 SITE 4 AC1 16 HIS A 340 HOH A 689 HOH A 764 HOH A 835 SITE 1 AC2 8 ASN A 164 PRO A 165 LYS A 258 PHE A 367 SITE 2 AC2 8 ASN A 373 SER A 375 HOH A 608 HOH A 702 SITE 1 AC3 6 GLY A 335 LYS A 336 GLY A 384 GLY A 385 SITE 2 AC3 6 ASN A 387 HOH A 603 CRYST1 37.273 50.398 114.497 90.00 90.00 90.00 P 2 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.026829 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019842 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008734 0.00000