HEADER HYDROLASE/HYDROLASE INHIBITOR 15-APR-93 1ARC TITLE THE PRIMARY STRUCTURE AND STRUCTURAL CHARACTERISTICS OF ACHROMOBACTER TITLE 2 LYTICUS PROTEASE I, A LYSINE-SPECIFIC SERINE PROTEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACHROMOBACTER PROTEASE I; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 206-473; COMPND 5 EC: 3.4.21.50; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACHROMOBACTER LYTICUS; SOURCE 3 ORGANISM_TAXID: 224 KEYWDS SERINE PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.KITAGAWA,Y.KATSUBE REVDAT 4 13-JUL-11 1ARC 1 VERSN REVDAT 3 12-MAY-09 1ARC 1 HET HETATM REVDAT 2 24-FEB-09 1ARC 1 VERSN REVDAT 1 31-OCT-93 1ARC 0 JRNL AUTH S.TSUNASAWA,T.MASAKI,M.HIROSE,M.SOEJIMA,F.SAKIYAMA JRNL TITL THE PRIMARY STRUCTURE AND STRUCTURAL CHARACTERISTICS OF JRNL TITL 2 ACHROMOBACTER LYTICUS PROTEASE I, A LYSINE-SPECIFIC SERINE JRNL TITL 3 PROTEASE. JRNL REF J.BIOL.CHEM. V. 264 3832 1989 JRNL REFN ISSN 0021-9258 JRNL PMID 2492988 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1924 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 72 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.014 ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ARC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. 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 : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL 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 : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL 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) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 42.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLY A 264 REMARK 465 GLY A 265 REMARK 465 GLY A 266 REMARK 465 THR A 267 REMARK 465 PRO A 268 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 OG SER A 194 C TCK A 270 1.95 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 TYR A 72 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 243 NE - CZ - NH2 ANGL. DEV. = -3.7 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 31 45.33 39.48 REMARK 500 ALA A 35 -58.91 -128.36 REMARK 500 ASN A 151 19.67 58.14 REMARK 500 ALA A 153 -166.20 -103.08 REMARK 500 VAL A 188 -147.06 -129.43 REMARK 500 LYS A 203 32.92 70.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: N-[(1S)-5-AMINO-1-(CHLOROACETYL)PENTYL]-4- REMARK 630 METHYLBENZENESULFONAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 TCK A 270 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: TSU LYS 0QE REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TCK A 270 DBREF 1ARC A 1 268 UNP P15636 API_ACHLY 206 473 SEQRES 1 A 268 GLY VAL SER GLY SER CYS ASN ILE ASP VAL VAL CYS PRO SEQRES 2 A 268 GLU GLY ASP GLY ARG ARG ASP ILE ILE ARG ALA VAL GLY SEQRES 3 A 268 ALA TYR SER LYS SER GLY THR LEU ALA CYS THR GLY SER SEQRES 4 A 268 LEU VAL ASN ASN THR ALA ASN ASP ARG LYS MET TYR PHE SEQRES 5 A 268 LEU THR ALA HIS HIS CYS GLY MET GLY THR ALA SER THR SEQRES 6 A 268 ALA ALA SER ILE VAL VAL TYR TRP ASN TYR GLN ASN SER SEQRES 7 A 268 THR CYS ARG ALA PRO ASN THR PRO ALA SER GLY ALA ASN SEQRES 8 A 268 GLY ASP GLY SER MET SER GLN THR GLN SER GLY SER THR SEQRES 9 A 268 VAL LYS ALA THR TYR ALA THR SER ASP PHE THR LEU LEU SEQRES 10 A 268 GLU LEU ASN ASN ALA ALA ASN PRO ALA PHE ASN LEU PHE SEQRES 11 A 268 TRP ALA GLY TRP ASP ARG ARG ASP GLN ASN TYR PRO GLY SEQRES 12 A 268 ALA ILE ALA ILE HIS HIS PRO ASN VAL ALA GLU LYS ARG SEQRES 13 A 268 ILE SER ASN SER THR SER PRO THR SER PHE VAL ALA TRP SEQRES 14 A 268 GLY GLY GLY ALA GLY THR THR HIS LEU ASN VAL GLN TRP SEQRES 15 A 268 GLN PRO SER GLY GLY VAL THR GLU PRO GLY SER SER GLY SEQRES 16 A 268 SER PRO ILE TYR SER PRO GLU LYS ARG VAL LEU GLY GLN SEQRES 17 A 268 LEU HIS GLY GLY PRO SER SER CYS SER ALA THR GLY THR SEQRES 18 A 268 ASN ARG SER ASP GLN TYR GLY ARG VAL PHE THR SER TRP SEQRES 19 A 268 THR GLY GLY GLY ALA ALA ALA SER ARG LEU SER ASP TRP SEQRES 20 A 268 LEU ASP PRO ALA SER THR GLY ALA GLN PHE ILE ASP GLY SEQRES 21 A 268 LEU ASP SER GLY GLY GLY THR PRO HET TCK A 270 20 HETNAM TCK N-[(1S)-5-AMINO-1-(CHLOROACETYL)PENTYL]-4- HETNAM 2 TCK METHYLBENZENESULFONAMIDE HETSYN TCK TOS-LYS-CH2CL FORMUL 2 TCK C14 H21 CL N2 O3 S FORMUL 3 HOH *72(H2 O) HELIX 1 1 CYS A 12 ASP A 16 5 5 HELIX 2 2 ASP A 20 ARG A 23 5 4 HELIX 3 3 HIS A 57 GLY A 59 5 3 HELIX 4 4 THR A 62 SER A 68 1 7 HELIX 5 5 THR A 85 ALA A 90 1 6 HELIX 6 6 ASN A 124 ASN A 128 5 5 HELIX 7 7 HIS A 149 ALA A 153 5 5 HELIX 8 8 THR A 219 ASN A 222 5 4 HELIX 9 9 VAL A 230 GLY A 236 1 7 HELIX 10 10 ALA A 239 ARG A 243 5 5 HELIX 11 11 LEU A 244 ASP A 249 1 6 SHEET 1 A 6 SER A 165 VAL A 167 0 SHEET 2 A 6 HIS A 177 GLN A 181 -1 N HIS A 177 O VAL A 167 SHEET 3 A 6 SER A 224 ARG A 229 -1 O ASP A 225 N VAL A 180 SHEET 4 A 6 ARG A 204 GLY A 211 -1 O GLN A 208 N GLY A 228 SHEET 5 A 6 GLY A 133 ASP A 135 1 O GLY A 133 N VAL A 205 SHEET 6 A 6 PHE A 257 ILE A 258 -1 N ILE A 258 O TRP A 134 SHEET 1 B 8 SER A 165 VAL A 167 0 SHEET 2 B 8 HIS A 177 GLN A 181 -1 N HIS A 177 O VAL A 167 SHEET 3 B 8 SER A 224 ARG A 229 -1 O ASP A 225 N VAL A 180 SHEET 4 B 8 ARG A 204 GLY A 211 -1 O GLN A 208 N GLY A 228 SHEET 5 B 8 PRO A 197 TYR A 199 -1 O ILE A 198 N LEU A 206 SHEET 6 B 8 ALA A 144 HIS A 148 -1 O ILE A 145 N TYR A 199 SHEET 7 B 8 ARG A 156 SER A 160 -1 N ARG A 156 O HIS A 148 SHEET 8 B 8 ILE A 8 ASP A 9 -1 O ILE A 8 N ILE A 157 SHEET 1 C 7 GLN A 98 SER A 101 0 SHEET 2 C 7 VAL A 70 TRP A 73 -1 N VAL A 71 O GLN A 100 SHEET 3 C 7 VAL A 25 LYS A 30 -1 O ALA A 27 N TYR A 72 SHEET 4 C 7 THR A 33 LEU A 40 -1 O THR A 33 N LYS A 30 SHEET 5 C 7 TYR A 51 ALA A 55 -1 N LEU A 53 O SER A 39 SHEET 6 C 7 PHE A 114 LEU A 119 -1 O THR A 115 N THR A 54 SHEET 7 C 7 SER A 103 TYR A 109 -1 O THR A 104 N GLU A 118 SHEET 1 D 2 PHE A 130 TRP A 131 0 SHEET 2 D 2 LEU A 261 ASP A 262 -1 O LEU A 261 N TRP A 131 SSBOND 1 CYS A 6 CYS A 216 1555 1555 1.99 SSBOND 2 CYS A 12 CYS A 80 1555 1555 2.04 SSBOND 3 CYS A 36 CYS A 58 1555 1555 2.05 LINK NE2 HIS A 57 CM TCK A 270 1555 1555 1.35 SITE 1 AC1 13 ALA A 45 ASN A 46 HIS A 57 TRP A 169 SITE 2 AC1 13 THR A 189 PRO A 191 GLY A 192 SER A 194 SITE 3 AC1 13 HIS A 210 GLY A 211 GLY A 212 SER A 214 SITE 4 AC1 13 ASP A 225 CRYST1 37.300 42.800 48.000 120.10 112.80 68.50 P 1 1 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 0.026810 -0.010561 0.007538 0.00000 SCALE2 0.000000 0.025112 0.011592 0.00000 SCALE3 0.000000 0.000000 0.024891 0.00000