HEADER HYDROLASE 29-OCT-20 7KLD TITLE CRYSTAL STRUCTURE OF AN ESSENTIAL RIBOSOMAL PROCESSING PROTEASE PRP TITLE 2 FROM S. AUREUS IN COMPLEX WITH A COVALENTLY LINKED PRODUCT PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHAGE-RELATED RIBOSOMAL PROTEASE; COMPND 3 CHAIN: A, B, D; COMPND 4 SYNONYM: RIBOSOMAL-PROCESSING CYSTEINE PROTEASE PRP,RIBOSOME- COMPND 5 ASSOCIATED PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: ELECTRON DENSITY IS MISSING FOR RESIDUES 24 - 29 IN COMPND 8 CHAIN A; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: LYS-LEU-ASN-LEU-GLN-PHE-PCS; COMPND 11 CHAIN: C, E, Q; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: AMINO TERMINAL K IS ACETYLATED PCS CHLOROKETONE: IN COMPND 14 THIS STRUCTURE THE SG OF CYS34 IN CHAINS A,B,C DISPLACES THE CHLORINE COMPND 15 TO FORM A COVALENT THIOTHER BOND. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: BN1321_260284, BTN44_03930, C7P97_01985, CSC87_06715, SOURCE 5 DD547_01729, DDL17_04735, DQV20_11645, DQV53_09155, E3A28_00240, SOURCE 6 E3K14_08315, E4U00_05990, EP54_09330, EQ90_02345, ERS072840_00776, SOURCE 7 FA040_12870, FVP29_06750, G0V24_11265, G0X12_13445, G0X27_07880, SOURCE 8 G0Y02_04565, G0Z08_03095, G0Z18_03180, G6W67_00930, G6W97_12315, SOURCE 9 G6X24_04030, G6X31_01365, G6X35_09650, G6Y10_03065, G6Y24_01400, SOURCE 10 G6Y28_11445, G6Y30_16890, GF545_03610, GF559_00535, GIX97_04380, SOURCE 11 GO677_13485, GO706_06595, GO746_11035, GO788_00935, GO793_02925, SOURCE 12 GO793_12515, GO803_01985, GO805_05045, GO810_16085, GO821_00235, SOURCE 13 GO894_13395, GO915_03870, GO941_09805, GO942_04925, SOURCE 14 HMPREF3211_01798, M1K003_1397, NCTC10654_01710, NCTC10702_02585, SOURCE 15 NCTC5664_03624, NCTC6133_02188, NCTC7878_03165, RK64_08805, SOURCE 16 SAMEA1029528_01686, SAMEA1029547_02076, SAMEA1029553_02519, SOURCE 17 SAMEA1469856_00607, SAMEA1469884_01223, SAMEA1531680_00288, SOURCE 18 SAMEA1531701_01205, SAMEA1964876_02447, SAMEA1965205_02481, SOURCE 19 SAMEA1966505_02490, SAMEA1969349_02416, SAMEA1969845_01676, SOURCE 20 SAMEA1971706_01055, SAMEA1972827_01838, SAMEA2076212_01600, SOURCE 21 SAMEA2076218_01666, SAMEA2076220_01752, SAMEA2076226_01556, SOURCE 22 SAMEA2076463_02381, SAMEA2076464_02394, SAMEA2076470_02431, SOURCE 23 SAMEA2076472_02346, SAMEA2076478_02402, SAMEA2076480_02456, SOURCE 24 SAMEA2076481_02468, SAMEA2076743_02501, SAMEA2076745_02445, SOURCE 25 SAMEA2076746_02444, SAMEA2076747_02486, SAMEA2076749_02400, SOURCE 26 SAMEA2076751_02425, SAMEA2076752_02493, SAMEA2076755_02464, SOURCE 27 SAMEA2076756_02514, SAMEA2076758_02521, SAMEA2076759_02515, SOURCE 28 SAMEA2076761_02557, SAMEA2076762_01945, SAMEA2076763_01877, SOURCE 29 SAMEA2076764_02486, SAMEA2076765_02396, SAMEA2077023_02451, SOURCE 30 SAMEA2077025_02500, SAMEA2077027_02451, SAMEA2077029_02463, SOURCE 31 SAMEA2077031_02497, SAMEA2077034_01994, SAMEA2077035_02483, SOURCE 32 SAMEA2077039_02486, SAMEA2077040_02404, SAMEA2077041_02447, SOURCE 33 SAMEA2077044_02452, SAMEA2077045_02427, SAMEA2077046_02417, SOURCE 34 SAMEA2077293_02510, SAMEA2077294_02438, SAMEA2077295_02425, SOURCE 35 SAMEA2077297_02396, SAMEA2077300_02477, SAMEA2077301_02476, SOURCE 36 SAMEA2077302_02443, SAMEA2077303_02458, SAMEA2077307_02357, SOURCE 37 SAMEA2077832_02485, SAMEA2078252_02489, SAMEA2078256_02457, SOURCE 38 SAMEA2078307_02502, SAMEA2078308_02409, SAMEA2078553_02399, SOURCE 39 SAMEA2078558_02472, SAMEA2078560_02496, SAMEA2078569_00046, SOURCE 40 SAMEA2078570_02413, SAMEA2078572_02514, SAMEA2078824_02435, SOURCE 41 SAMEA2078837_02548, SAMEA2079048_02570, SAMEA2079051_02465, SOURCE 42 SAMEA2079277_01808, SAMEA2079291_02682, SAMEA2079503_02553, SOURCE 43 SAMEA2079507_01005, SAMEA2079512_02667, SAMEA2079517_02674, SOURCE 44 SAMEA2079724_01337, SAMEA2079727_01612, SAMEA2079728_01943, SOURCE 45 SAMEA2079732_01656, SAMEA2079742_01684, SAMEA2079946_01624, SOURCE 46 SAMEA2079949_01591, SAMEA2079951_01555, SAMEA2079952_01419, SOURCE 47 SAMEA2079957_01912, SAMEA2079958_01822, SAMEA2079960_01835, SOURCE 48 SAMEA2079961_01609, SAMEA2079968_01340, SAMEA2080329_01468, SOURCE 49 SAMEA2080330_01912, SAMEA2080334_01932, SAMEA2080433_01740, SOURCE 50 SAMEA2080812_02522, SAMEA2080898_02518, SAMEA2080900_02445, SOURCE 51 SAMEA2080904_02459, SAMEA2080913_02507, SAMEA2081043_02492, SOURCE 52 SAMEA2081053_02569, SAMEA2081054_02533, SAMEA2081055_02521, SOURCE 53 SAMEA2081060_01823, SAMEA2081211_00857, SAMEA2081213_00881, SOURCE 54 SAMEA2081218_01649, SAMEA2081341_01341, SAMEA2081342_01612, SOURCE 55 SAMEA2081349_01864, SAMEA2081359_01619, SAMEA2081362_01623, SOURCE 56 SAMEA2081468_02419, SAMEA2081474_02496, SAMEA2081475_02467, SOURCE 57 SAMEA2081476_02433, SAMEA2081479_02517, SAMEA2081480_02464, SOURCE 58 SAMEA2081560_02361, SAMEA2081561_02437, SAMEA2081564_02416, SOURCE 59 SAMEA2081567_02404, SAMEA2081568_02500, SAMEA2081569_02476, SOURCE 60 SAMEA2081570_02367, SAMEA2081571_02441, SAMEA2081572_02441, SOURCE 61 SAMEA2081573_02444, SAMEA2081575_02417, SAMEA2081577_02472, SOURCE 62 SAMEA2081578_02440, SAMEA2081579_02464, SAMEA2081581_02376, SOURCE 63 SAMEA2081582_02553, SAMEA2081673_01456, SAMEA2081674_01693, SOURCE 64 SAMEA958766_01141, SAMEA958770_01541, SAMEA958772_01367, SOURCE 65 SAMEA958778_01377, SAMEA958779_02720, SAMEA958785_01190, SOURCE 66 SAMEA958793_01565, SAMEA958798_01254, SAMEA958804_01429, SOURCE 67 SAMEA958810_02901, SAMEA958836_01614, SAMEA958838_02812, SOURCE 68 SAMEA958845_01498, SAMEA958846_01744, SAMEA958848_02333, SOURCE 69 SAMEA958855_02126, SAMEA958858_02293, SAMEA958870_02489, SOURCE 70 SAMEA958898_01783, SAMEA958906_02170, SAMEA958924_01277, SOURCE 71 SAMEA958925_01299, SAMEA958951_01296, SAMEA958953_00896, SOURCE 72 SAMEA958961_01996, SAMEA958979_01146, SAMEA958987_02151, SOURCE 73 SAMEA958995_01155, SAST44_01826, SAST45_01804; SOURCE 74 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 75 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 76 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS (DE3)-RIL; SOURCE 77 EXPRESSION_SYSTEM_PLASMID: PEW34; SOURCE 78 MOL_ID: 2; SOURCE 79 SYNTHETIC: YES; SOURCE 80 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 81 ORGANISM_TAXID: 1280; SOURCE 82 OTHER_DETAILS: AMINO TERMINAL PEPTIDE OF RIBOSOMAL PROTEIN L27 KEYWDS CYSTEINE PROTEASE RIBOSOMAL PROTEIN L27, HYDROLASE, PRODUCT COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.T.WRIGHT,D.PETERSON REVDAT 3 25-OCT-23 7KLD 1 REMARK REVDAT 2 15-FEB-23 7KLD 1 JRNL REVDAT 1 01-SEP-21 7KLD 0 JRNL AUTH J.A.HOTINGER,H.A.PENDERGRASS,D.PETERSON,H.T.WRIGHT,A.E.MAY JRNL TITL PHAGE-RELATED RIBOSOMAL PROTEASE (PRP) OF STAPHYLOCOCCUS JRNL TITL 2 AUREUS : IN VITRO MICHAELIS-MENTEN KINETICS, SCREENING FOR JRNL TITL 3 INHIBITORS, AND CRYSTAL STRUCTURE OF A COVALENT INHIBITION JRNL TITL 4 PRODUCT COMPLEX. JRNL REF BIOCHEMISTRY V. 61 1323 2022 JRNL REFN ISSN 0006-2960 JRNL PMID 35731716 JRNL DOI 10.1021/ACS.BIOCHEM.2C00010 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 15160 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 774 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 29.3100 - 4.0900 0.99 2442 135 0.2493 0.2723 REMARK 3 2 4.0800 - 3.2400 1.00 2416 122 0.2221 0.2605 REMARK 3 3 3.2400 - 2.8300 1.00 2400 129 0.2500 0.2773 REMARK 3 4 2.8300 - 2.5800 1.00 2387 134 0.2568 0.2848 REMARK 3 5 2.5800 - 2.3900 1.00 2406 126 0.2636 0.3312 REMARK 3 6 2.3900 - 2.2500 0.99 2335 128 0.2582 0.2863 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.213 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.884 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.13 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 : 0.020 2526 REMARK 3 ANGLE : 1.835 3451 REMARK 3 CHIRALITY : 0.117 415 REMARK 3 PLANARITY : 0.011 458 REMARK 3 DIHEDRAL : 17.801 886 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7KLD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1000252628. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : RIGAKU VARIMAX-HF ARC REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER R 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO 40.64.42A REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15213 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 29.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.14800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.8400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.90 REMARK 200 R MERGE FOR SHELL (I) : 0.60200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.400 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: 4PEO REMARK 200 REMARK 200 REMARK: PRISM REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SAMPLE: 10 - 20 MG/ML IN 10MM REMARK 280 HEPES (PH 7.5), 0.1M NACL, 0.3MM TCEP, 3.3MM TRISS (PH 7.5), 0.5% REMARK 280 BETA-OCTYLGLUCOSIDE, <4% GLYCEROL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,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 15.88290 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.27800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.44382 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 15.88290 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.27800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 45.44382 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: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -223.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 -15.88290 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 -33.27800 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -45.44382 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 15.88290 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 -33.27800 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 45.44382 REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE SUBSTRATE-LIKE CYSTEINE PROTEASE INHIBITOR IS PEPTIDE-LIKE, A REMARK 400 MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: SUBSTRATE-LIKE CYSTEINE PROTEASE INHIBITOR REMARK 400 CHAIN: C, E, Q REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 ASP A 24 REMARK 465 HIS A 25 REMARK 465 GLY A 26 REMARK 465 GLU A 27 REMARK 465 TYR A 28 REMARK 465 GLY A 29 REMARK 465 LYS E 1 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 HIS A 30 CG ND1 CD2 CE1 NE2 REMARK 470 ASN A 63 CG OD1 ND2 REMARK 470 ARG A 70 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 95 CD OE1 OE2 REMARK 470 GLU B 27 CG CD OE1 OE2 REMARK 470 TYR B 28 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 HIS B 30 CG ND1 CD2 CE1 NE2 REMARK 470 ASP B 62 CG OD1 OD2 REMARK 470 GLN B 91 CG CD OE1 NE2 REMARK 470 GLU B 95 CG CD OE1 OE2 REMARK 470 GLU B 99 CG CD OE1 OE2 REMARK 470 LYS C 1 CG CD CE NZ REMARK 470 GLU D 27 CG CD OE1 OE2 REMARK 470 TYR D 28 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 HIS D 30 CG ND1 CD2 CE1 NE2 REMARK 470 ASP D 31 CG OD1 OD2 REMARK 470 ASP D 62 OD1 OD2 REMARK 470 ASN D 63 CG OD1 ND2 REMARK 470 ARG D 70 NH1 NH2 REMARK 470 GLU D 95 CG CD OE1 OE2 REMARK 470 LYS Q 1 CG CD CE NZ 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 VAL A 72 -61.67 -99.63 REMARK 500 HIS B 30 11.72 -144.23 REMARK 500 HIS B 66 119.45 -161.63 REMARK 500 VAL B 72 -61.81 -99.32 REMARK 500 ASP D 62 -55.67 -6.06 REMARK 500 VAL D 72 -61.15 -100.55 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 337 DISTANCE = 6.89 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 CA D 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 8 O REMARK 620 2 HOH A 305 O 125.6 REMARK 620 3 HOH A 309 O 127.5 3.8 REMARK 620 4 HOH A 316 O 125.6 2.5 2.1 REMARK 620 5 ASP D 10 OD1 126.4 1.0 2.8 2.0 REMARK 620 6 ASP D 10 OD2 127.4 1.8 3.8 3.5 1.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 20 OD1 REMARK 620 2 ASP A 20 OD2 46.3 REMARK 620 3 HOH A 317 O 75.0 81.5 REMARK 620 4 ASP B 57 OD1 127.4 141.1 137.2 REMARK 620 5 ASP B 57 OD2 80.1 121.4 109.3 53.0 REMARK 620 6 ASN B 59 OD1 109.8 65.0 111.4 95.4 139.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 51 O REMARK 620 2 HOH A 320 O 76.7 REMARK 620 3 HOH A 321 O 102.0 178.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 203 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 57 OD1 REMARK 620 2 ASP A 57 OD2 53.0 REMARK 620 3 ASN A 59 OD1 95.5 146.3 REMARK 620 4 ASP B 20 OD1 169.8 128.8 79.9 REMARK 620 5 ASP B 20 OD2 137.2 84.7 127.2 47.7 REMARK 620 6 HOH B 311 O 96.6 108.4 84.6 92.0 90.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 204 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 94 OE2 REMARK 620 2 ASN A 98 O 101.0 REMARK 620 3 ILE A 101 O 99.8 80.8 REMARK 620 4 GLU B 11 OE1 140.4 115.6 100.6 REMARK 620 5 GLU B 11 OE2 137.1 116.6 105.7 5.2 REMARK 620 6 HOH B 301 O 99.8 84.1 157.1 70.8 66.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 104 OD1 REMARK 620 2 TYR A 105 O 82.7 REMARK 620 3 ASP B 10 OD1 122.1 128.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU B 51 O REMARK 620 2 GLU B 78 OE2 81.4 REMARK 620 3 HOH B 308 O 70.8 71.9 REMARK 620 4 HOH B 317 O 76.5 145.1 75.4 REMARK 620 5 HOH D 315 O 98.8 153.1 133.8 58.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA D 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP D 20 OD1 REMARK 620 2 ASP D 20 OD2 47.7 REMARK 620 3 ASP D 57 OD1 80.2 38.9 REMARK 620 4 ASP D 57 OD2 76.4 38.9 7.2 REMARK 620 5 ASN D 59 OD1 85.3 44.6 5.7 9.6 REMARK 620 6 HOH D 307 O 84.9 47.6 10.3 9.0 6.7 REMARK 620 N 1 2 3 4 5 DBREF 7KLD A 1 106 UNP W8U5D2 W8U5D2_STAAU 1 106 DBREF 7KLD B 1 106 UNP W8U5D2 W8U5D2_STAAU 1 106 DBREF 7KLD C 1 7 PDB 7KLD 7KLD 1 7 DBREF 7KLD D 1 106 UNP W8U5D2 W8U5D2_STAAU 1 106 DBREF 7KLD E 1 7 PDB 7KLD 7KLD 1 7 DBREF 7KLD Q 1 7 PDB 7KLD 7KLD 1 7 SEQRES 1 A 106 MET ILE THR VAL ASP ILE THR VAL ASN ASP GLU GLY LYS SEQRES 2 A 106 VAL THR ASP VAL ILE MET ASP GLY HIS ALA ASP HIS GLY SEQRES 3 A 106 GLU TYR GLY HIS ASP ILE VAL CYS ALA GLY ALA SER ALA SEQRES 4 A 106 VAL LEU PHE GLY SER VAL ASN ALA ILE ILE GLY LEU THR SEQRES 5 A 106 SER GLU ARG PRO ASP ILE ASN TYR ASP ASP ASN GLY GLY SEQRES 6 A 106 HIS PHE HIS ILE ARG SER VAL ASP THR ASN ASN ASP GLU SEQRES 7 A 106 ALA GLN LEU ILE LEU GLN THR MET LEU VAL SER LEU GLN SEQRES 8 A 106 THR ILE GLU GLU GLU TYR ASN GLU ASN ILE ARG LEU ASN SEQRES 9 A 106 TYR LYS SEQRES 1 B 106 MET ILE THR VAL ASP ILE THR VAL ASN ASP GLU GLY LYS SEQRES 2 B 106 VAL THR ASP VAL ILE MET ASP GLY HIS ALA ASP HIS GLY SEQRES 3 B 106 GLU TYR GLY HIS ASP ILE VAL CYS ALA GLY ALA SER ALA SEQRES 4 B 106 VAL LEU PHE GLY SER VAL ASN ALA ILE ILE GLY LEU THR SEQRES 5 B 106 SER GLU ARG PRO ASP ILE ASN TYR ASP ASP ASN GLY GLY SEQRES 6 B 106 HIS PHE HIS ILE ARG SER VAL ASP THR ASN ASN ASP GLU SEQRES 7 B 106 ALA GLN LEU ILE LEU GLN THR MET LEU VAL SER LEU GLN SEQRES 8 B 106 THR ILE GLU GLU GLU TYR ASN GLU ASN ILE ARG LEU ASN SEQRES 9 B 106 TYR LYS SEQRES 1 C 7 LYS LEU ASN LEU GLN PHE PCS SEQRES 1 D 106 MET ILE THR VAL ASP ILE THR VAL ASN ASP GLU GLY LYS SEQRES 2 D 106 VAL THR ASP VAL ILE MET ASP GLY HIS ALA ASP HIS GLY SEQRES 3 D 106 GLU TYR GLY HIS ASP ILE VAL CYS ALA GLY ALA SER ALA SEQRES 4 D 106 VAL LEU PHE GLY SER VAL ASN ALA ILE ILE GLY LEU THR SEQRES 5 D 106 SER GLU ARG PRO ASP ILE ASN TYR ASP ASP ASN GLY GLY SEQRES 6 D 106 HIS PHE HIS ILE ARG SER VAL ASP THR ASN ASN ASP GLU SEQRES 7 D 106 ALA GLN LEU ILE LEU GLN THR MET LEU VAL SER LEU GLN SEQRES 8 D 106 THR ILE GLU GLU GLU TYR ASN GLU ASN ILE ARG LEU ASN SEQRES 9 D 106 TYR LYS SEQRES 1 E 7 LYS LEU ASN LEU GLN PHE PCS SEQRES 1 Q 7 LYS LEU ASN LEU GLN PHE PCS HET PCS C 7 23 HET PCS E 7 23 HET PCS Q 7 23 HET CA A 201 1 HET CA A 202 1 HET CA A 203 1 HET CA A 204 1 HET CA B 201 1 HET CA B 202 1 HET CA D 201 1 HET CA D 202 1 HETNAM PCS PHENYLALANYLMETHYLCHLORIDE HETNAM CA CALCIUM ION FORMUL 3 PCS 3(C10 H12 CL N O) FORMUL 7 CA 8(CA 2+) FORMUL 15 HOH *87(H2 O) HELIX 1 AA1 ASP A 31 THR A 52 1 22 HELIX 2 AA2 ASN A 76 TYR A 97 1 22 HELIX 3 AA3 ASP B 31 THR B 52 1 22 HELIX 4 AA4 ASN B 76 TYR B 97 1 22 HELIX 5 AA5 ASP D 31 THR D 52 1 22 HELIX 6 AA6 ASN D 76 TYR D 97 1 22 SHEET 1 AA1 5 ASP A 57 TYR A 60 0 SHEET 2 AA1 5 HIS A 66 ARG A 70 -1 O HIS A 68 N ASN A 59 SHEET 3 AA1 5 VAL A 14 ASP A 20 -1 N VAL A 17 O ILE A 69 SHEET 4 AA1 5 ILE A 2 VAL A 8 -1 N THR A 3 O ASP A 20 SHEET 5 AA1 5 ILE A 101 TYR A 105 1 O ASN A 104 N ILE A 6 SHEET 1 AA2 5 ASP B 57 TYR B 60 0 SHEET 2 AA2 5 HIS B 66 ARG B 70 -1 O HIS B 68 N ASN B 59 SHEET 3 AA2 5 VAL B 14 ASP B 20 -1 N VAL B 17 O ILE B 69 SHEET 4 AA2 5 ILE B 2 VAL B 8 -1 N THR B 7 O ASP B 16 SHEET 5 AA2 5 ILE B 101 TYR B 105 1 O ASN B 104 N VAL B 4 SHEET 1 AA3 5 ASP D 57 TYR D 60 0 SHEET 2 AA3 5 HIS D 66 ARG D 70 -1 O HIS D 68 N ASN D 59 SHEET 3 AA3 5 VAL D 14 ASP D 20 -1 N VAL D 17 O ILE D 69 SHEET 4 AA3 5 ILE D 2 VAL D 8 -1 N ASP D 5 O ILE D 18 SHEET 5 AA3 5 ILE D 101 TYR D 105 1 O ASN D 104 N VAL D 4 LINK SG CYS A 34 CT PCS Q 7 1555 1555 1.74 LINK SG CYS B 34 CT PCS C 7 1555 1555 1.81 LINK C PHE C 6 N PCS C 7 1555 1555 1.34 LINK SG CYS D 34 CT PCS E 7 1555 1555 1.81 LINK C PHE E 6 N PCS E 7 1555 1555 1.34 LINK C PHE Q 6 N PCS Q 7 1555 1555 1.33 LINK O VAL A 8 CA CA D 202 1555 4545 2.50 LINK OD1 ASP A 20 CA CA B 202 1555 1555 2.45 LINK OD2 ASP A 20 CA CA B 202 1555 1555 3.02 LINK O LEU A 51 CA CA A 202 1555 1555 2.80 LINK OD1 ASP A 57 CA CA A 203 1555 1555 2.55 LINK OD2 ASP A 57 CA CA A 203 1555 1555 2.27 LINK OD1 ASN A 59 CA CA A 203 1555 1555 2.06 LINK OE2 GLU A 94 CA CA A 204 1555 1555 2.36 LINK O ASN A 98 CA CA A 204 1555 1555 2.15 LINK O ILE A 101 CA CA A 204 1555 1555 2.42 LINK OD1 ASN A 104 CA CA A 201 1555 1555 2.74 LINK O TYR A 105 CA CA A 201 1555 1555 2.52 LINK CA CA A 201 OD1 ASP B 10 2555 1555 2.26 LINK CA CA A 202 O HOH A 320 1555 1555 2.14 LINK CA CA A 202 O HOH A 321 1555 2455 2.17 LINK CA CA A 203 OD1 ASP B 20 1555 1555 2.83 LINK CA CA A 203 OD2 ASP B 20 1555 1555 2.43 LINK CA CA A 203 O HOH B 311 1555 1555 3.18 LINK CA CA A 204 OE1 GLU B 11 2555 1555 2.29 LINK CA CA A 204 OE2 GLU B 11 2555 1555 2.49 LINK CA CA A 204 O HOH B 301 1555 2555 2.52 LINK O HOH A 305 CA CA D 202 4555 1555 1.97 LINK O HOH A 309 CA CA D 202 4555 1555 2.04 LINK O HOH A 316 CA CA D 202 4555 1555 1.94 LINK O HOH A 317 CA CA B 202 1555 1555 2.10 LINK O LEU B 51 CA CA B 201 1555 1555 2.82 LINK OD1 ASP B 57 CA CA B 202 1555 1555 2.30 LINK OD2 ASP B 57 CA CA B 202 1555 1555 2.71 LINK OD1 ASN B 59 CA CA B 202 1555 1555 2.03 LINK OE2 GLU B 78 CA CA B 201 1555 1555 2.88 LINK CA CA B 201 O HOH B 308 1555 1555 2.28 LINK CA CA B 201 O HOH B 317 1555 1555 2.61 LINK CA CA B 201 O HOH D 315 1555 1555 2.35 LINK OD1 ASP D 10 CA CA D 202 1555 1555 2.72 LINK OD2 ASP D 10 CA CA D 202 1555 1555 2.61 LINK OD1 ASP D 20 CA CA D 201 1555 2656 2.50 LINK OD2 ASP D 20 CA CA D 201 1555 2656 2.71 LINK OD1 ASP D 57 CA CA D 201 1555 1555 2.69 LINK OD2 ASP D 57 CA CA D 201 1555 1555 2.38 LINK OD1 ASN D 59 CA CA D 201 1555 1555 2.01 LINK CA CA D 201 O HOH D 307 1555 1555 2.17 CRYST1 53.482 66.556 93.446 90.00 103.44 90.00 I 1 2 1 12 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 0.018698 0.000000 0.004468 0.00000 SCALE2 0.000000 0.015025 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011003 0.00000