HEADER HYDROLASE 08-DEC-08 3FH4 TITLE CRYSTAL STRUCTURE OF RECOMBINANT VIBRIO PROTEOLYTICUS AMINOPEPTIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIAL LEUCYL AMINOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.11.10; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PROTEOLYTICUS; SOURCE 3 ORGANISM_TAXID: 671; SOURCE 4 STRAIN: IFO13287; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 STAR (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET26B(+) KEYWDS RECOMBINANT VIBRIO PROTEOLYTICUS AMINOPEPTIDASE, AMINOPEPTIDASE, KEYWDS 2 HYDROLASE, METAL-BINDING, PROTEASE, SECRETED, ZINC, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR W.YONG,J.-J.P.KIM,M.HARTLEY,B.BENNETT REVDAT 2 06-SEP-23 3FH4 1 REMARK LINK REVDAT 1 17-NOV-09 3FH4 0 JRNL AUTH M.HARTLEY,B.BENNETT JRNL TITL HETEROLOGOUS EXPRESSION AND PURIFICATION OF VIBRIO JRNL TITL 2 PROTEOLYTICUS (AEROMONAS PROTEOLYTICA) AMINOPEPTIDASE: A JRNL TITL 3 RAPID PROTOCOL JRNL REF PROTEIN EXPR.PURIF. V. 66 91 2009 JRNL REFN ISSN 1046-5928 JRNL PMID 19233285 JRNL DOI 10.1016/J.PEP.2009.02.011 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 21990 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 + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1168 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1631 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.2410 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2210 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.41 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.169 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.096 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.355 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2298 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3139 ; 1.083 ; 1.930 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 296 ; 5.560 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 104 ;35.533 ;25.481 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 347 ;12.788 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;15.244 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 348 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1784 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1203 ; 0.192 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1615 ; 0.297 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 162 ; 0.124 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.081 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 33 ; 0.202 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.197 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1469 ; 0.454 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2367 ; 0.855 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 867 ; 1.279 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 772 ; 2.038 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3FH4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000050583. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 98 REMARK 200 PH : 8.0 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23158 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 41.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 21.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.13500 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 21.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.51500 REMARK 200 FOR SHELL : 31.50 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: PDB ENTRY 2IQ6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VPAP (0.5 MM) IN 10 MM TRIS BUFFER, PH REMARK 280 8.0, CONTAINING 10 MM KSCN AND 400 MM NACL WAS EQUILIBRATED WITH REMARK 280 100 MM TRIS BUFFER, PH 8.0, CONTAINING 100 MM KSCN AND 4.5 M REMARK 280 NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.17633 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 62.35267 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 46.76450 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 77.94083 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 15.58817 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 31.17633 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 62.35267 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 77.94083 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 46.76450 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 15.58817 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 373 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 421 LIES ON A SPECIAL POSITION. 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 292 REMARK 465 THR A 293 REMARK 465 PRO A 294 REMARK 465 THR A 295 REMARK 465 PRO A 296 REMARK 465 GLY A 297 REMARK 465 ASN A 298 REMARK 465 GLN A 299 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 MET A 180 101.18 82.24 REMARK 500 ASN A 252 109.65 -39.20 REMARK 500 SER A 265 -144.12 -96.86 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 A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 97 NE2 REMARK 620 2 ASP A 117 OD1 97.3 REMARK 620 3 ASP A 179 OD1 99.7 92.9 REMARK 620 4 ASP A 179 OD2 92.5 150.6 58.0 REMARK 620 5 TRS A 302 O1 109.5 107.5 141.3 95.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 117 OD2 REMARK 620 2 GLU A 152 OE1 154.1 REMARK 620 3 GLU A 152 OE2 96.8 57.5 REMARK 620 4 HIS A 256 NE2 95.9 85.9 98.1 REMARK 620 5 TRS A 302 O1 101.9 84.3 94.0 157.1 REMARK 620 6 TRS A 302 N 100.4 105.5 160.6 89.2 73.7 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 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IQ6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE AMINOPEPTIDASE FROM VIBRIO PROTEOLYTICUS REMARK 900 IN COMPLEXATION WITH LEUCYL-LEUCYL-LEUCINE DBREF 3FH4 A 1 299 UNP Q01693 AMPX_VIBPR 107 405 SEQRES 1 A 299 MET PRO PRO ILE THR GLN GLN ALA THR VAL THR ALA TRP SEQRES 2 A 299 LEU PRO GLN VAL ASP ALA SER GLN ILE THR GLY THR ILE SEQRES 3 A 299 SER SER LEU GLU SER PHE THR ASN ARG PHE TYR THR THR SEQRES 4 A 299 THR SER GLY ALA GLN ALA SER ASP TRP ILE ALA SER GLU SEQRES 5 A 299 TRP GLN ALA LEU SER ALA SER LEU PRO ASN ALA SER VAL SEQRES 6 A 299 LYS GLN VAL SER HIS SER GLY TYR ASN GLN LYS SER VAL SEQRES 7 A 299 VAL MET THR ILE THR GLY SER GLU ALA PRO ASP GLU TRP SEQRES 8 A 299 ILE VAL ILE GLY GLY HIS LEU ASP SER THR ILE GLY SER SEQRES 9 A 299 HIS THR ASN GLU GLN SER VAL ALA PRO GLY ALA ASP ASP SEQRES 10 A 299 ASP ALA SER GLY ILE ALA ALA VAL THR GLU VAL ILE ARG SEQRES 11 A 299 VAL LEU SER GLU ASN ASN PHE GLN PRO LYS ARG SER ILE SEQRES 12 A 299 ALA PHE MET ALA TYR ALA ALA GLU GLU VAL GLY LEU ARG SEQRES 13 A 299 GLY SER GLN ASP LEU ALA ASN GLN TYR LYS SER GLU GLY SEQRES 14 A 299 LYS ASN VAL VAL SER ALA LEU GLN LEU ASP MET THR ASN SEQRES 15 A 299 TYR LYS GLY SER ALA GLN ASP VAL VAL PHE ILE THR ASP SEQRES 16 A 299 TYR THR ASP SER ASN PHE THR GLN TYR LEU THR GLN LEU SEQRES 17 A 299 MET ASP GLU TYR LEU PRO SER LEU THR TYR GLY PHE ASP SEQRES 18 A 299 THR CYS GLY TYR ALA CYS SER ASP HIS ALA SER TRP HIS SEQRES 19 A 299 ASN ALA GLY TYR PRO ALA ALA MET PRO PHE GLU SER LYS SEQRES 20 A 299 PHE ASN ASP TYR ASN PRO ARG ILE HIS THR THR GLN ASP SEQRES 21 A 299 THR LEU ALA ASN SER ASP PRO THR GLY SER HIS ALA LYS SEQRES 22 A 299 LYS PHE THR GLN LEU GLY LEU ALA TYR ALA ILE GLU MET SEQRES 23 A 299 GLY SER ALA THR GLY ASP THR PRO THR PRO GLY ASN GLN HET ZN A 300 1 HET ZN A 301 1 HET TRS A 302 8 HET NA A 303 1 HET NA A 304 1 HETNAM ZN ZINC ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM NA SODIUM ION HETSYN TRS TRIS BUFFER FORMUL 2 ZN 2(ZN 2+) FORMUL 4 TRS C4 H12 N O3 1+ FORMUL 5 NA 2(NA 1+) FORMUL 7 HOH *150(H2 O) HELIX 1 1 GLN A 6 LEU A 14 1 9 HELIX 2 2 PRO A 15 VAL A 17 5 3 HELIX 3 3 ASP A 18 SER A 31 1 14 HELIX 4 4 THR A 39 ALA A 58 1 20 HELIX 5 5 ASP A 118 ASN A 135 1 18 HELIX 6 6 ALA A 150 GLY A 154 5 5 HELIX 7 7 LEU A 155 GLU A 168 1 14 HELIX 8 8 ASP A 198 LEU A 213 1 16 HELIX 9 9 ASP A 229 ALA A 236 1 8 HELIX 10 10 LYS A 247 TYR A 251 5 5 HELIX 11 11 THR A 261 SER A 265 5 5 HELIX 12 12 GLY A 269 ALA A 289 1 21 SHEET 1 A 8 ALA A 63 VAL A 68 0 SHEET 2 A 8 SER A 77 ILE A 82 -1 O SER A 77 N VAL A 68 SHEET 3 A 8 ARG A 141 TYR A 148 -1 O PHE A 145 N MET A 80 SHEET 4 A 8 ALA A 87 HIS A 97 1 N ILE A 92 O ALA A 144 SHEET 5 A 8 ASN A 171 GLN A 177 1 O ASN A 171 N TRP A 91 SHEET 6 A 8 ALA A 240 PHE A 244 1 O ALA A 241 N GLN A 177 SHEET 7 A 8 VAL A 190 ILE A 193 -1 N VAL A 191 O PHE A 244 SHEET 8 A 8 TYR A 218 ASP A 221 1 O GLY A 219 N PHE A 192 SSBOND 1 CYS A 223 CYS A 227 1555 1555 2.01 LINK NE2 HIS A 97 ZN ZN A 301 1555 1555 2.09 LINK OD2 ASP A 117 ZN ZN A 300 1555 1555 2.07 LINK OD1 ASP A 117 ZN ZN A 301 1555 1555 1.94 LINK OE1 GLU A 152 ZN ZN A 300 1555 1555 2.37 LINK OE2 GLU A 152 ZN ZN A 300 1555 1555 2.15 LINK OD1 ASP A 179 ZN ZN A 301 1555 1555 2.08 LINK OD2 ASP A 179 ZN ZN A 301 1555 1555 2.40 LINK OG SER A 215 NA NA A 304 1555 1555 2.93 LINK NE2 HIS A 256 ZN ZN A 300 1555 1555 2.14 LINK ZN ZN A 300 O1 TRS A 302 1555 1555 2.25 LINK ZN ZN A 300 N TRS A 302 1555 1555 2.31 LINK ZN ZN A 301 O1 TRS A 302 1555 1555 2.13 CISPEP 1 ASP A 117 ASP A 118 0 -1.21 SITE 1 AC1 5 ASP A 117 GLU A 152 HIS A 256 ZN A 301 SITE 2 AC1 5 TRS A 302 SITE 1 AC2 6 HIS A 97 ASP A 117 GLU A 151 ASP A 179 SITE 2 AC2 6 ZN A 300 TRS A 302 SITE 1 AC3 11 HIS A 97 ASP A 117 GLU A 151 GLU A 152 SITE 2 AC3 11 ASP A 179 MET A 180 TYR A 225 CYS A 227 SITE 3 AC3 11 HIS A 256 ZN A 300 ZN A 301 SITE 1 AC4 3 THR A 38 TYR A 73 ASN A 74 SITE 1 AC5 3 LEU A 213 PRO A 214 SER A 215 CRYST1 108.397 108.397 93.529 90.00 90.00 120.00 P 61 2 2 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 0.009225 0.005326 0.000000 0.00000 SCALE2 0.000000 0.010653 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010692 0.00000