HEADER HYDROLASE 16-NOV-04 1Y0R TITLE CRYSTAL STRUCTURE OF THE TETRAHEDRAL AMINOPEPTIDASE FROM P. HORIKOSHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: FRV OPERON PROTEIN FRVX; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRSET 6C KEYWDS AMINOPEPTIDASE DOMAIN, PDZ DOMAIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.GROLL,L.BORISSENKO REVDAT 4 13-MAR-24 1Y0R 1 REMARK LINK REVDAT 3 13-JUL-11 1Y0R 1 VERSN REVDAT 2 24-FEB-09 1Y0R 1 VERSN REVDAT 1 01-MAR-05 1Y0R 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. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1245052.050 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.2 REMARK 3 NUMBER OF REFLECTIONS : 41238 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) : 0.210 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2149 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5695 REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 335 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2578 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.80 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.13 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.890 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) : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 63.64 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 : 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 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Y0R 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_1000030970. 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) : 1.278, 1.2828, 1.05, 1.0 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 : 59987 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 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 <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) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: DM 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, 2 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: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PQS 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -298.0 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 350 BIOMT1 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 3 -1.000000 0.000000 0.000000 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 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 465 LYS A 352 REMARK 465 ILE A 353 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 CE NZ REMARK 480 LYS A 62 CE NZ REMARK 480 LYS A 81 CE NZ REMARK 480 LYS A 111 NZ REMARK 480 LYS A 157 CD CE NZ REMARK 480 LYS A 173 CD CE NZ REMARK 480 LYS A 195 CD CE NZ REMARK 480 LYS A 198 CD CE NZ REMARK 480 ASP A 199 CB CG OD1 OD2 REMARK 480 GLU A 227 CG CD OE1 OE2 REMARK 480 GLU A 247 CG CD OE1 OE2 REMARK 480 LYS A 249 CE NZ REMARK 480 LYS A 256 CD CE NZ REMARK 480 ARG A 265 CD NE CZ NH1 NH2 REMARK 480 GLY A 295 C O REMARK 480 GLU A 350 CG CD OE1 OE2 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 O HOH A 1042 O HOH A 1162 2555 0.39 REMARK 500 OE2 GLU A 10 NH2 ARG A 170 3556 2.11 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 GLU A 59 50.63 -96.74 REMARK 500 VAL A 251 -67.03 69.95 REMARK 500 LYS A 307 -119.94 46.71 REMARK 500 HIS A 323 54.40 74.42 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 86.8 REMARK 620 3 ASP A 235 OD2 97.4 151.4 REMARK 620 4 ASP A 235 OD1 118.1 99.0 54.1 REMARK 620 5 ARS A1003 AS 133.9 104.2 93.3 104.4 REMARK 620 N 1 2 3 4 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 100.0 REMARK 620 3 GLU A 213 OE1 154.3 55.0 REMARK 620 4 HIS A 323 NE2 97.0 116.4 90.6 REMARK 620 5 ARS A1003 AS 90.1 120.8 107.3 119.9 REMARK 620 N 1 2 3 4 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 RESIDUE ARS A 1003 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: 1Y0Y RELATED DB: PDB REMARK 900 TETRAHEDRAL AMINOPEPTIDASE IN COMPLEX WITH AMASTATIN DBREF 1Y0R A 1 353 UNP O59196 O59196_PYRHO 1 353 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 HET ZN A1001 1 HET ZN A1002 1 HET ARS A1003 1 HETNAM ZN ZINC ION HETNAM ARS ARSENIC FORMUL 2 ZN 2(ZN 2+) FORMUL 4 ARS AS FORMUL 5 HOH *160(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 GLN A 101 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 NE2 HIS A 68 ZN ZN A1001 1555 1555 2.43 LINK OD1 ASP A 182 ZN ZN A1001 1555 1555 1.97 LINK OD2 ASP A 182 ZN ZN A1002 1555 1555 2.14 LINK OE2 GLU A 213 ZN ZN A1002 1555 1555 2.23 LINK OE1 GLU A 213 ZN ZN A1002 1555 1555 2.50 LINK OD2 ASP A 235 ZN ZN A1001 1555 1555 2.54 LINK OD1 ASP A 235 ZN ZN A1001 1555 1555 2.24 LINK NE2 HIS A 323 ZN ZN A1002 1555 1555 2.38 LINK ZN ZN A1001 AS ARS A1003 1555 1555 3.04 LINK ZN ZN A1002 AS ARS A1003 1555 1555 3.08 CISPEP 1 ASP A 182 ASP A 183 0 0.19 SITE 1 AC1 4 HIS A 68 ASP A 182 ASP A 235 ARS A1003 SITE 1 AC2 4 ASP A 182 GLU A 213 HIS A 323 ARS A1003 SITE 1 AC3 4 GLU A 212 GLY A 297 ZN A1001 ZN A1002 CRYST1 111.572 111.572 111.572 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 0.008963 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008963 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008963 0.00000