HEADER ANTIMICROBIAL PROTEIN 26-OCT-18 6I0I TITLE STRUCTURE OF THE STREPTOMYCES SUBTILISIN AND TAMP INHIBITOR (SSTI) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSGLUTAMINASE-ACTIVATING METALLOPROTEASE INHIBITOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TAMEP INHIBITOR,P14; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES MOBARAENSIS NBRC 13819 = DSM SOURCE 3 40847; SOURCE 4 ORGANISM_COMMON: STREPTOVERTICILLIUM MOBARAENSE; SOURCE 5 ORGANISM_TAXID: 1223523; SOURCE 6 GENE: STI; SOURCE 7 EXPRESSION_SYSTEM: STREPTOMYCES MOBARAENSIS NBRC 13819 = DSM 40847; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 1223523 KEYWDS MTG, MICROBIAL TRANSGLUTAMINASE; SIL, SSI-LIKE INHIBITORY PROTEIN; KEYWDS 2 SSI, STREPTOMYCES SUBTILISIN INHIBITOR; SSTI, STREPTOMYCES KEYWDS 3 SUBTILISIN AND TAMP INHIBITOR; TAMP, TRANSGLUTAMINASE-ACTIVATING KEYWDS 4 METALLOPROTEASE; TAP, TRIPEPTIDYLAMINOPEPTIDASE., ANTIMICROBIAL KEYWDS 5 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.SCHMELZ,N.E.JUETTNER,H.L.FUCHSBAUER,A.SCRIMA REVDAT 4 23-OCT-24 6I0I 1 REMARK REVDAT 3 24-JAN-24 6I0I 1 REMARK REVDAT 2 26-FEB-20 6I0I 1 JRNL REVDAT 1 04-SEP-19 6I0I 0 JRNL AUTH N.E.JUETTNER,S.SCHMELZ,A.ANDERL,F.COLIN,M.CLASSEN,F.PFEIFER, JRNL AUTH 2 A.SCRIMA,H.L.FUCHSBAUER JRNL TITL THE N-TERMINAL PEPTIDE OF THE TRANSGLUTAMINASE-ACTIVATING JRNL TITL 2 METALLOPROTEASE INHIBITOR FROM STREPTOMYCES MOBARAENSIS JRNL TITL 3 ACCOMMODATES BOTH INHIBITION AND GLUTAMINE CROSS-LINKING JRNL TITL 4 SITES. JRNL REF FEBS J. V. 287 708 2020 JRNL REFN ISSN 1742-464X JRNL PMID 31420998 JRNL DOI 10.1111/FEBS.15044 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 35513 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1748 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 44.7662 - 3.3154 0.99 2955 116 0.1442 0.1631 REMARK 3 2 3.3154 - 2.6316 1.00 2861 143 0.1623 0.2095 REMARK 3 3 2.6316 - 2.2990 1.00 2820 174 0.1842 0.2237 REMARK 3 4 2.2990 - 2.0888 1.00 2830 148 0.1703 0.2391 REMARK 3 5 2.0888 - 1.9391 1.00 2791 155 0.1806 0.2006 REMARK 3 6 1.9391 - 1.8247 1.00 2809 149 0.1990 0.2267 REMARK 3 7 1.8247 - 1.7333 1.00 2863 129 0.2277 0.2452 REMARK 3 8 1.7333 - 1.6579 1.00 2768 154 0.2478 0.2850 REMARK 3 9 1.6579 - 1.5941 1.00 2814 136 0.2586 0.3123 REMARK 3 10 1.5941 - 1.5391 1.00 2831 137 0.2791 0.3003 REMARK 3 11 1.5391 - 1.4909 1.00 2783 158 0.3135 0.3035 REMARK 3 12 1.4909 - 1.4483 0.94 2640 149 0.3484 0.3846 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.19 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 : 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 6I0I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1200012561. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918409 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS BUILT=20180126 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35535 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 44.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 1.09500 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: 2SIC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3 M NACITRATE 50 MM HEPES 7.5 REMARK 280 14MG/ML PROTEIN, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 17.57650 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 LYS B 63 REMARK 465 SER B 64 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 ALA A 4 168.20 73.05 REMARK 500 ASN A 73 66.97 -154.37 REMARK 500 REMARK 500 REMARK: NULL DBREF 6I0I A 3 110 UNP P83544 SSIT_STRMB 41 148 DBREF 6I0I B 3 110 UNP P83544 SSIT_STRMB 41 148 SEQRES 1 A 108 TYR ALA PRO SER ALA LEU VAL LEU THR VAL GLY GLN GLY SEQRES 2 A 108 ASP LYS ALA ALA SER ALA GLY VAL GLN ARG ALA VAL THR SEQRES 3 A 108 LEU ASN CYS MET PRO LYS PRO SER GLY THR HIS PRO ASP SEQRES 4 A 108 ALA ARG GLY ALA CYS ASP GLN LEU ARG ALA ALA SER GLY SEQRES 5 A 108 ASN PHE ALA GLU ILE THR LYS ILE LYS SER GLY THR ALA SEQRES 6 A 108 CYS THR LYS GLU TRP ASN PRO PHE VAL VAL THR ALA GLU SEQRES 7 A 108 GLY VAL TRP GLU GLY GLN ARG VAL LYS TYR GLU HIS THR SEQRES 8 A 108 PHE ALA ASN PRO CYS GLU MET LYS ALA GLY LYS GLY THR SEQRES 9 A 108 VAL PHE GLU PHE SEQRES 1 B 108 TYR ALA PRO SER ALA LEU VAL LEU THR VAL GLY GLN GLY SEQRES 2 B 108 ASP LYS ALA ALA SER ALA GLY VAL GLN ARG ALA VAL THR SEQRES 3 B 108 LEU ASN CYS MET PRO LYS PRO SER GLY THR HIS PRO ASP SEQRES 4 B 108 ALA ARG GLY ALA CYS ASP GLN LEU ARG ALA ALA SER GLY SEQRES 5 B 108 ASN PHE ALA GLU ILE THR LYS ILE LYS SER GLY THR ALA SEQRES 6 B 108 CYS THR LYS GLU TRP ASN PRO PHE VAL VAL THR ALA GLU SEQRES 7 B 108 GLY VAL TRP GLU GLY GLN ARG VAL LYS TYR GLU HIS THR SEQRES 8 B 108 PHE ALA ASN PRO CYS GLU MET LYS ALA GLY LYS GLY THR SEQRES 9 B 108 VAL PHE GLU PHE FORMUL 3 HOH *284(H2 O) HELIX 1 AA1 LYS A 17 ALA A 21 5 5 HELIX 2 AA2 ASP A 41 ALA A 52 1 12 HELIX 3 AA3 ASN A 55 LYS A 61 1 7 HELIX 4 AA4 ASN A 96 LYS A 104 1 9 HELIX 5 AA5 LYS B 17 ALA B 21 5 5 HELIX 6 AA6 ASP B 41 ALA B 52 1 12 HELIX 7 AA7 ASN B 55 LYS B 61 1 7 HELIX 8 AA8 ASN B 96 LYS B 104 1 9 SHEET 1 AA1 4 GLY A 22 ASN A 30 0 SHEET 2 AA1 4 ALA A 7 GLN A 14 -1 N LEU A 8 O LEU A 29 SHEET 3 AA1 4 PHE A 75 TRP A 83 -1 O VAL A 82 N ALA A 7 SHEET 4 AA1 4 GLN A 86 PHE A 94 -1 O PHE A 94 N PHE A 75 SHEET 1 AA2 4 GLY B 22 ASN B 30 0 SHEET 2 AA2 4 ALA B 7 GLN B 14 -1 N VAL B 12 O GLN B 24 SHEET 3 AA2 4 PHE B 75 TRP B 83 -1 O VAL B 82 N ALA B 7 SHEET 4 AA2 4 GLN B 86 PHE B 94 -1 O PHE B 94 N PHE B 75 SSBOND 1 CYS A 31 CYS A 46 1555 1555 2.04 SSBOND 2 CYS A 68 CYS A 98 1555 1555 2.05 SSBOND 3 CYS B 31 CYS B 46 1555 1555 2.03 SSBOND 4 CYS B 68 CYS B 98 1555 1555 2.04 CISPEP 1 MET A 32 PRO A 33 0 -1.93 CISPEP 2 MET B 32 PRO B 33 0 -2.70 CRYST1 46.481 35.153 64.016 90.00 105.71 90.00 P 1 21 1 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 0.021514 0.000000 0.006051 0.00000 SCALE2 0.000000 0.028447 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016227 0.00000