PDB Short entry for 1Y0Y HEADER HYDROLASE/HYDROLASE INHIBITOR 16-NOV-04 1Y0Y TITLE CRYSTAL STRUCTURE OF TETRAHEDRAL AMINOPEPTIDASE FROM P. HORIKOSHII IN TITLE 2 COMPLEX WITH AMASTATIN CAVEAT 1Y0Y CHIRALITY ERROR AT CA CENTER OF VAL B 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FRV OPERON PROTEIN FRVX; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: AMASTATIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PRSET 6C; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: STREPTOMYCES SP. ME98-M3 KEYWDS AMINOPEPTIDASE, PDZ, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.GROLL,L.BORISSENKO REVDAT 5 15-NOV-23 1Y0Y 1 REMARK LINK ATOM REVDAT 4 12-DEC-12 1Y0Y 1 ATOM CAVEAT COMPND DBREF REVDAT 4 2 1 HEADER KEYWDS LINK SITE REVDAT 3 13-JUL-11 1Y0Y 1 VERSN REVDAT 2 24-FEB-09 1Y0Y 1 VERSN REVDAT 1 01-MAR-05 1Y0Y 0 JRNL AUTH L.BORISSENKO,M.GROLL JRNL TITL CRYSTAL STRUCTURE OF TET PROTEASE REVEALS COMPLEMENTARY JRNL TITL 2 PROTEIN DEGRADATION PATHWAYS IN PROKARYOTES JRNL REF J.MOL.BIOL. V. 346 1207 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15713475 JRNL DOI 10.1016/J.JMB.2004.12.056 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2348489.790 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 60171 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 SET) : 0.206 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3031 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 9171 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 465 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2629 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.820 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.090 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.720 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.850 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.850 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 64.58 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : AMA.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Y0Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030977. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MPG/DESY, HAMBURG REMARK 200 BEAMLINE : BW6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.05 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL, NON REMARK 200 DISPERSIVE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60465 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.44800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: CNS 1.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, PH 6.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 3 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,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X 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 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS GENERATED: REMARK 300 X,Y,Z; X,-Y,-Z; -X,Y,-Z; REMARK 300 -X,-Y,Z; Z,X,Y; -Z,-X,Y; REMARK 300 Z,-X,-Y; -Z,X,-Y; Y,Z,X; REMARK 300 -Y,Z,-X; -Y,-Z,X; Y,-Z,-X 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: 24-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 24-MERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 59990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 124230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1218.0 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 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 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT2 8 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT1 9 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 9 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 9 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 10 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 11 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 12 1.000000 0.000000 0.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE AMASTATIN IS PEPTIDE-LIKE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: AMASTATIN REMARK 400 CHAIN: B 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 VAL A 3 REMARK 465 ARG A 4 REMARK 465 ASN A 5 REMARK 465 VAL A 120 REMARK 465 PRO A 121 REMARK 465 PRO A 122 REMARK 465 HIS A 123 REMARK 465 ILE A 124 REMARK 465 GLN A 125 REMARK 465 LYS A 126 REMARK 465 PRO A 127 REMARK 465 GLU A 128 REMARK 465 ASP A 129 REMARK 465 ARG A 130 REMARK 465 LYS A 131 REMARK 465 LYS A 132 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 48 CG CD CE NZ REMARK 480 LYS A 81 CD CE NZ REMARK 480 LYS A 111 CD CE NZ REMARK 480 ASP A 135 CB CG OD1 OD2 REMARK 480 LYS A 157 CE NZ REMARK 480 LYS A 173 CD CE NZ REMARK 480 LYS A 198 CD CE NZ REMARK 480 GLU A 247 CD OE1 OE2 REMARK 480 LYS A 256 NZ REMARK 480 ARG A 265 CD NE CZ NH1 NH2 REMARK 480 GLU A 339 CD OE1 OE2 REMARK 480 GLU A 350 CG CD OE1 OE2 REMARK 480 LYS A 352 CB CG CD CE NZ REMARK 480 ASP B 4 O CG OD1 OD2 OXT 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 O PHE A 181 N ASP A 183 2.16 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 ASP B 4 C ASP B 4 OXT 0.117 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 L2O B 1 CA - C - N ANGL. DEV. = 15.3 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 ASP A 182 85.52 -52.12 REMARK 500 ASP A 183 -8.50 78.12 REMARK 500 VAL A 251 -66.37 69.51 REMARK 500 LYS A 307 -118.89 44.42 REMARK 500 HIS A 323 60.37 68.18 REMARK 500 VAL B 3 -87.10 96.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 L2O B 1 VAL B 2 142.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 L2O B 1 -19.49 REMARK 500 REMARK 500 REMARK: NULL 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 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 68 NE2 REMARK 620 2 ASP A 182 OD1 90.6 REMARK 620 3 ASP A 235 OD2 92.3 153.3 REMARK 620 4 ASP A 235 OD1 107.2 98.8 55.0 REMARK 620 5 L2O B 1 O1 93.7 91.9 114.4 156.3 REMARK 620 6 L2O B 1 N 163.2 105.9 74.4 73.8 83.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 182 OD2 REMARK 620 2 GLU A 213 OE2 99.4 REMARK 620 3 GLU A 213 OE1 153.5 56.8 REMARK 620 4 HIS A 323 NE2 84.9 104.7 90.1 REMARK 620 5 L2O B 1 O1 100.5 91.3 92.2 162.2 REMARK 620 6 L2O B 1 O 122.4 138.0 82.7 84.2 78.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF AMASTATIN REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XFO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FRVX REMARK 900 RELATED ID: 1VHE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A AMINOPEPTIDASE/GLUCANASE HOMOLOG REMARK 900 RELATED ID: 1VHO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A PUTATIVE PEPTIDASE/ENDOGLUCANASE REMARK 900 RELATED ID: 1Y0R RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TET FROM P. HORIKOSHII, NATIVE DBREF 1Y0Y A 1 353 UNP O59196 O59196_PYRHO 1 353 DBREF 1Y0Y B 1 4 PDB 1Y0Y 1Y0Y 1 4 SEQRES 1 A 353 MET GLU VAL ARG ASN MET VAL ASP TYR GLU LEU LEU LYS SEQRES 2 A 353 LYS VAL VAL GLU ALA PRO GLY VAL SER GLY TYR GLU PHE SEQRES 3 A 353 LEU GLY ILE ARG ASP VAL VAL ILE GLU GLU ILE LYS ASP SEQRES 4 A 353 TYR VAL ASP GLU VAL LYS VAL ASP LYS LEU GLY ASN VAL SEQRES 5 A 353 ILE ALA HIS LYS LYS GLY GLU GLY PRO LYS VAL MET ILE SEQRES 6 A 353 ALA ALA HIS MET ASP GLN ILE GLY LEU MET VAL THR HIS SEQRES 7 A 353 ILE GLU LYS ASN GLY PHE LEU ARG VAL ALA PRO ILE GLY SEQRES 8 A 353 GLY VAL ASP PRO LYS THR LEU ILE ALA GLN ARG PHE LYS SEQRES 9 A 353 VAL TRP ILE ASP LYS GLY LYS PHE ILE TYR GLY VAL GLY SEQRES 10 A 353 ALA SER VAL PRO PRO HIS ILE GLN LYS PRO GLU ASP ARG SEQRES 11 A 353 LYS LYS ALA PRO ASP TRP ASP GLN ILE PHE ILE ASP ILE SEQRES 12 A 353 GLY ALA GLU SER LYS GLU GLU ALA GLU ASP MET GLY VAL SEQRES 13 A 353 LYS ILE GLY THR VAL ILE THR TRP ASP GLY ARG LEU GLU SEQRES 14 A 353 ARG LEU GLY LYS HIS ARG PHE VAL SER ILE ALA PHE ASP SEQRES 15 A 353 ASP ARG ILE ALA VAL TYR THR ILE LEU GLU VAL ALA LYS SEQRES 16 A 353 GLN LEU LYS ASP ALA LYS ALA ASP VAL TYR PHE VAL ALA SEQRES 17 A 353 THR VAL GLN GLU GLU VAL GLY LEU ARG GLY ALA ARG THR SEQRES 18 A 353 SER ALA PHE GLY ILE GLU PRO ASP TYR GLY PHE ALA ILE SEQRES 19 A 353 ASP VAL THR ILE ALA ALA ASP ILE PRO GLY THR PRO GLU SEQRES 20 A 353 HIS LYS GLN VAL THR HIS LEU GLY LYS GLY THR ALA ILE SEQRES 21 A 353 LYS ILE MET ASP ARG SER VAL ILE CYS HIS PRO THR ILE SEQRES 22 A 353 VAL ARG TRP LEU GLU GLU LEU ALA LYS LYS HIS GLU ILE SEQRES 23 A 353 PRO TYR GLN LEU GLU ILE LEU LEU GLY GLY GLY THR ASP SEQRES 24 A 353 ALA GLY ALA ILE HIS LEU THR LYS ALA GLY VAL PRO THR SEQRES 25 A 353 GLY ALA LEU SER VAL PRO ALA ARG TYR ILE HIS SER ASN SEQRES 26 A 353 THR GLU VAL VAL ASP GLU ARG ASP VAL ASP ALA THR VAL SEQRES 27 A 353 GLU LEU MET THR LYS ALA LEU GLU ASN ILE HIS GLU LEU SEQRES 28 A 353 LYS ILE SEQRES 1 B 4 L2O VAL VAL ASP HET L2O B 1 10 HET ZN A1001 1 HET ZN A1002 1 HETNAM L2O (2S,3R)-3-AMINO-2-HYDROXY-5-METHYLHEXANOIC ACID HETNAM ZN ZINC ION FORMUL 2 L2O C7 H15 N O3 FORMUL 3 ZN 2(ZN 2+) FORMUL 5 HOH *210(H2 O) HELIX 1 1 ASP A 8 ALA A 18 1 11 HELIX 2 2 TYR A 24 LEU A 27 5 4 HELIX 3 3 GLY A 28 LYS A 38 1 11 HELIX 4 4 ASP A 39 VAL A 41 5 3 HELIX 5 5 ASP A 94 LEU A 98 5 5 HELIX 6 6 ASP A 135 ILE A 139 5 5 HELIX 7 7 SER A 147 MET A 154 1 8 HELIX 8 8 ALA A 180 LEU A 197 1 18 HELIX 9 9 LEU A 216 GLU A 227 1 12 HELIX 10 10 PRO A 246 GLN A 250 5 5 HELIX 11 11 HIS A 270 HIS A 284 1 15 HELIX 12 12 ASP A 299 HIS A 304 1 6 HELIX 13 13 GLU A 331 ILE A 348 1 18 HELIX 14 14 HIS A 349 LEU A 351 5 3 SHEET 1 A 8 GLU A 43 VAL A 46 0 SHEET 2 A 8 VAL A 52 LYS A 56 -1 O ILE A 53 N LYS A 45 SHEET 3 A 8 ASP A 203 THR A 209 -1 O PHE A 206 N ALA A 54 SHEET 4 A 8 LYS A 62 HIS A 68 1 N ILE A 65 O VAL A 207 SHEET 5 A 8 TYR A 230 ILE A 238 1 O PHE A 232 N ALA A 66 SHEET 6 A 8 THR A 312 ALA A 319 1 O ALA A 319 N THR A 237 SHEET 7 A 8 THR A 258 ASP A 264 -1 N ALA A 259 O SER A 316 SHEET 8 A 8 VAL A 267 ILE A 268 -1 O VAL A 267 N ASP A 264 SHEET 1 B 8 GLU A 43 VAL A 46 0 SHEET 2 B 8 VAL A 52 LYS A 56 -1 O ILE A 53 N LYS A 45 SHEET 3 B 8 ASP A 203 THR A 209 -1 O PHE A 206 N ALA A 54 SHEET 4 B 8 LYS A 62 HIS A 68 1 N ILE A 65 O VAL A 207 SHEET 5 B 8 TYR A 230 ILE A 238 1 O PHE A 232 N ALA A 66 SHEET 6 B 8 THR A 312 ALA A 319 1 O ALA A 319 N THR A 237 SHEET 7 B 8 THR A 258 ASP A 264 -1 N ALA A 259 O SER A 316 SHEET 8 B 8 TYR A 288 ILE A 292 1 O GLU A 291 N ILE A 262 SHEET 1 C 7 GLY A 73 ILE A 79 0 SHEET 2 C 7 LEU A 85 ILE A 90 -1 O ILE A 90 N GLY A 73 SHEET 3 C 7 PHE A 140 ASP A 142 -1 O ILE A 141 N LEU A 85 SHEET 4 C 7 LYS A 111 ALA A 118 -1 N VAL A 116 O ASP A 142 SHEET 5 C 7 ARG A 102 ASP A 108 -1 N VAL A 105 O ILE A 113 SHEET 6 C 7 VAL A 161 TRP A 164 -1 O THR A 163 N LYS A 104 SHEET 7 C 7 GLY A 73 ILE A 79 -1 N LEU A 74 O ILE A 162 SHEET 1 D 3 GLU A 169 LEU A 171 0 SHEET 2 D 3 ARG A 175 SER A 178 -1 O ARG A 175 N LEU A 171 SHEET 3 D 3 GLU A 327 ASP A 330 -1 O GLU A 327 N SER A 178 LINK C L2O B 1 N VAL B 2 1555 1555 1.38 LINK NE2 HIS A 68 ZN ZN A1001 1555 1555 2.26 LINK OD1 ASP A 182 ZN ZN A1001 1555 1555 2.14 LINK OD2 ASP A 182 ZN ZN A1002 1555 1555 2.12 LINK OE2 GLU A 213 ZN ZN A1002 1555 1555 2.18 LINK OE1 GLU A 213 ZN ZN A1002 1555 1555 2.41 LINK OD2 ASP A 235 ZN ZN A1001 1555 1555 2.42 LINK OD1 ASP A 235 ZN ZN A1001 1555 1555 2.31 LINK NE2 HIS A 323 ZN ZN A1002 1555 1555 2.15 LINK ZN ZN A1001 O1 L2O B 1 1555 1555 2.05 LINK ZN ZN A1001 N L2O B 1 1555 1555 2.17 LINK ZN ZN A1002 O1 L2O B 1 1555 1555 2.11 LINK ZN ZN A1002 O L2O B 1 1555 1555 2.38 SITE 1 AC1 5 HIS A 68 ASP A 182 ASP A 235 ZN A1002 SITE 2 AC1 5 L2O B 1 SITE 1 AC2 5 ASP A 182 GLU A 213 HIS A 323 ZN A1001 SITE 2 AC2 5 L2O B 1 SITE 1 AC3 14 HIS A 68 ASP A 182 GLU A 212 GLU A 213 SITE 2 AC3 14 ASP A 235 VAL A 236 LEU A 293 GLY A 296 SITE 3 AC3 14 GLY A 297 ILE A 322 HIS A 323 ZN A1001 SITE 4 AC3 14 ZN A1002 HOH B 101 CRYST1 111.560 111.560 111.560 90.00 90.00 90.00 P 2 3 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 0.008964 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008964 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008964 0.00000