HEADER HYDROLASE 15-JUN-06 2HC9 TITLE STRUCTURE OF CAENORHABDITIS ELEGANS LEUCINE AMINOPEPTIDASE-ZINC TITLE 2 COMPLEX (LAP1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCINE AMINOPEPTIDASE 1; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.11.1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: LAP-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 AI; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET3 KEYWDS PEPTIDASE, CARBONATE, STRUCTURAL GENOMICS, AMINOPEPTIDASE, PSI, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR KEYWDS 3 STRUCTURAL GENOMICS, NYSGXRC, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.ZHAN,Y.PATSKOVSKY,B.C.WENGERTER,U.RAMAGOPAL,S.MILSTEIN,M.VIDAL, AUTHOR 2 S.C.ALMO,S.K.BURLEY,NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL AUTHOR 3 GENOMICS (NYSGXRC) REVDAT 6 30-AUG-23 2HC9 1 REMARK REVDAT 5 20-OCT-21 2HC9 1 SEQADV REVDAT 4 03-FEB-21 2HC9 1 AUTHOR REMARK LINK REVDAT 3 13-JUL-11 2HC9 1 VERSN REVDAT 2 24-FEB-09 2HC9 1 VERSN REVDAT 1 15-AUG-06 2HC9 0 JRNL AUTH C.ZHAN,Y.PATSKOVSKY,B.C.WENGERTER,U.RAMAGOPAL,S.MILSTEIN, JRNL AUTH 2 M.VIDAL,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE AND FUNCTION OF CAENORHABDITIS ELEGANS JRNL TITL 2 LEUCINE AMINOPEPTIDASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 53285 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) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1701 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3866 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.1850 REMARK 3 BIN FREE R VALUE SET COUNT : 129 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3665 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 113 REMARK 3 SOLVENT ATOMS : 667 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.34000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : -0.51000 REMARK 3 B12 (A**2) : 0.17000 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): 0.096 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.955 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3964 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5377 ; 1.364 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 527 ; 7.095 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 150 ;34.760 ;24.933 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 675 ;12.899 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;20.381 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 618 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2901 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2090 ; 0.192 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2692 ; 0.308 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 957 ; 0.189 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.070 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 107 ; 0.180 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 99 ; 0.221 ; 0.500 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): 2494 ; 2.508 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4034 ; 3.419 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1495 ; 4.002 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1327 ; 5.613 ; 3.000 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 2HC9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000038187. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55114 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : 0.04300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.46100 REMARK 200 R SYM FOR SHELL (I) : 0.41200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 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: 2HB6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS, 2 M AMMONIUM SULFATE, PH REMARK 280 8.5, 10% GLYCEROL, 200 MM SODIUM CHLORIDE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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 REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 0.00000 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 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 63.17200 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 63.17200 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 63.17200 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 0.00000 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 0.00000 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 63.17200 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 63.17200 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 63.17200 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 53250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 87760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -786.0 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 -0.500000 -0.866025 0.000000 -131.30900 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -65.65450 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -113.71693 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 -65.65450 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 -113.71693 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 63.17200 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 -131.30900 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 63.17200 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 63.17200 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 A2197 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2466 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 MET A 1 REMARK 465 GLN A 491 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 PRO A 60 -165.74 -67.17 REMARK 500 GLU A 70 -19.54 -152.65 REMARK 500 ASN A 271 -8.81 87.42 REMARK 500 ASP A 317 -25.70 109.53 REMARK 500 ALA A 335 54.88 -95.95 REMARK 500 ALA A 406 72.40 -150.78 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 702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 252 NZ REMARK 620 2 ASP A 257 OD2 171.8 REMARK 620 3 ASP A 275 OD2 103.6 82.3 REMARK 620 4 GLU A 336 OE1 100.3 83.8 101.3 REMARK 620 5 HOH A2159 O 99.1 72.9 141.0 105.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 257 OD2 REMARK 620 2 ASP A 334 O 178.2 REMARK 620 3 ASP A 334 OD1 95.7 84.9 REMARK 620 4 GLU A 336 OE2 97.3 83.6 128.3 REMARK 620 5 HOH A2159 O 86.8 91.4 124.6 106.0 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 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BCT A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1008 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1009 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1010 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1011 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1012 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1013 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1014 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1015 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1016 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HB6 RELATED DB: PDB REMARK 900 STRUCTURE OF CAENORHABDITIS ELEGANS LEUCINE AMINOPEPTIDASE REMARK 900 RELATED ID: NYSGXRC-T2217 RELATED DB: TARGETDB DBREF 2HC9 A 1 491 UNP P34629 AMPL_CAEEL 1 491 SEQADV 2HC9 LEU A 440 UNP P34629 PHE 440 ENGINEERED MUTATION SEQRES 1 A 491 MET THR GLN VAL LEU VAL ARG ASN GLY ILE GLN ALA VAL SEQRES 2 A 491 GLY ASP GLY LEU THR SER LEU ILE ILE VAL GLY LYS LYS SEQRES 3 A 491 SER VAL LEU LYS ASN VAL THR PHE GLU GLY LYS PHE LYS SEQRES 4 A 491 GLU VAL ALA GLN LYS PHE VAL THR ASP GLY ASP SER TRP SEQRES 5 A 491 ASN SER MET ILE SER ARG ILE PRO ALA SER GLY ARG HIS SEQRES 6 A 491 PRO LEU HIS TYR GLU LEU ALA HIS LEU ILE THR VAL PRO SEQRES 7 A 491 ASP ALA SER SER ARG GLY ASN THR PRO THR ASN ALA HIS SEQRES 8 A 491 SER ILE TYR LYS GLU LEU LYS PRO ILE ASN TYR PRO GLU SEQRES 9 A 491 ASP THR LYS ASN VAL HIS PHE VAL LEU PHE ALA GLU TYR SEQRES 10 A 491 PRO ASP VAL LEU SER HIS VAL ALA ALA ILE ALA ARG THR SEQRES 11 A 491 PHE CYS LYS PHE SER MET LYS THR SER GLY ILE ARG GLU SEQRES 12 A 491 LEU ASN VAL ASN ILE ASP VAL VAL CYS ASP LYS LEU THR SEQRES 13 A 491 ASN GLU ASP ALA VAL PHE LEU THR ASP LEU SER GLU SER SEQRES 14 A 491 VAL ARG GLU THR ALA ARG LEU ILE ASP THR PRO ALA ASN SEQRES 15 A 491 ILE LEU THR THR ASP ALA LEU VAL ASP GLU ALA VAL LYS SEQRES 16 A 491 VAL GLY ASN ALA THR GLY SER LYS ILE THR VAL ILE ARG SEQRES 17 A 491 GLY GLU GLU LEU LEU LYS ALA GLY PHE GLY GLY ILE TYR SEQRES 18 A 491 HIS VAL GLY LYS ALA GLY PRO THR PRO PRO ALA PHE VAL SEQRES 19 A 491 VAL LEU SER HIS GLU VAL PRO GLY SER THR GLU HIS ILE SEQRES 20 A 491 ALA LEU VAL GLY LYS GLY VAL VAL TYR ASP THR GLY GLY SEQRES 21 A 491 LEU GLN ILE LYS THR LYS THR GLY MET PRO ASN MET LYS SEQRES 22 A 491 ARG ASP MET GLY GLY ALA ALA GLY MET LEU GLU ALA TYR SEQRES 23 A 491 SER ALA LEU VAL LYS HIS GLY PHE SER GLN THR LEU HIS SEQRES 24 A 491 ALA CYS LEU CYS ILE VAL GLU ASN ASN VAL SER PRO ILE SEQRES 25 A 491 ALA ASN LYS PRO ASP ASP ILE ILE LYS MET LEU SER GLY SEQRES 26 A 491 LYS THR VAL GLU ILE ASN ASN THR ASP ALA GLU GLY ARG SEQRES 27 A 491 LEU ILE LEU ALA ASP GLY VAL PHE TYR ALA LYS GLU THR SEQRES 28 A 491 LEU LYS ALA THR THR ILE PHE ASP MET ALA THR LEU THR SEQRES 29 A 491 GLY ALA GLN ALA TRP LEU SER GLY ARG LEU HIS GLY ALA SEQRES 30 A 491 ALA MET THR ASN ASP GLU GLN LEU GLU ASN GLU ILE ILE SEQRES 31 A 491 LYS ALA GLY LYS ALA SER GLY ASP LEU VAL ALA PRO MET SEQRES 32 A 491 LEU PHE ALA PRO ASP LEU PHE PHE GLY ASP LEU LYS SER SEQRES 33 A 491 SER ILE ALA ASP MET LYS ASN SER ASN LEU GLY LYS MET SEQRES 34 A 491 ASP GLY PRO PRO SER ALA VAL ALA GLY LEU LEU ILE GLY SEQRES 35 A 491 ALA HIS ILE GLY PHE GLY GLU GLY LEU ARG TRP LEU HIS SEQRES 36 A 491 LEU ASP ILE ALA ALA PRO ALA GLU VAL GLY ASP ARG GLY SEQRES 37 A 491 THR GLY TYR GLY PRO ALA LEU PHE SER THR LEU LEU GLY SEQRES 38 A 491 LYS TYR THR SER VAL PRO MET LEU LYS GLN HET ZN A 701 1 HET ZN A 702 1 HET BCT A 801 4 HET SO4 A 901 5 HET SO4 A 902 5 HET NA A2001 1 HET GOL A1001 6 HET GOL A1002 6 HET GOL A1003 6 HET GOL A1004 6 HET GOL A1005 6 HET GOL A1006 6 HET GOL A1007 6 HET GOL A1008 6 HET GOL A1009 6 HET GOL A1010 6 HET GOL A1011 6 HET GOL A1012 6 HET GOL A1013 6 HET GOL A1014 6 HET GOL A1015 6 HET GOL A1016 6 HETNAM ZN ZINC ION HETNAM BCT BICARBONATE ION HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN 2(ZN 2+) FORMUL 4 BCT C H O3 1- FORMUL 5 SO4 2(O4 S 2-) FORMUL 7 NA NA 1+ FORMUL 8 GOL 16(C3 H8 O3) FORMUL 24 HOH *667(H2 O) HELIX 1 1 LYS A 26 VAL A 32 1 7 HELIX 2 2 GLU A 35 GLN A 43 1 9 HELIX 3 3 ASP A 48 ILE A 59 1 12 HELIX 4 4 ASN A 89 LYS A 98 1 10 HELIX 5 5 GLU A 116 PRO A 118 5 3 HELIX 6 6 ASP A 119 ARG A 129 1 11 HELIX 7 7 THR A 156 THR A 179 1 24 HELIX 8 8 THR A 185 THR A 200 1 16 HELIX 9 9 GLY A 209 GLY A 216 1 8 HELIX 10 10 PHE A 217 LYS A 225 1 9 HELIX 11 11 ASN A 271 ASP A 275 5 5 HELIX 12 12 MET A 276 LYS A 291 1 16 HELIX 13 13 GLU A 336 THR A 351 1 16 HELIX 14 14 ALA A 366 GLY A 372 1 7 HELIX 15 15 ASP A 382 GLY A 397 1 16 HELIX 16 16 ALA A 406 PHE A 411 1 6 HELIX 17 17 GLY A 412 LYS A 415 5 4 HELIX 18 18 PRO A 432 ALA A 443 1 12 HELIX 19 19 HIS A 444 GLU A 449 5 6 HELIX 20 20 GLY A 472 GLY A 481 1 10 HELIX 21 21 LYS A 482 THR A 484 5 3 HELIX 22 22 VAL A 486 LYS A 490 5 5 SHEET 1 A 6 GLN A 3 ASN A 8 0 SHEET 2 A 6 ASN A 145 VAL A 151 1 O VAL A 146 N GLN A 3 SHEET 3 A 6 ASN A 108 PHE A 114 1 N PHE A 111 O ASN A 147 SHEET 4 A 6 THR A 18 LYS A 25 1 N SER A 19 O HIS A 110 SHEET 5 A 6 ALA A 72 VAL A 77 1 O ILE A 75 N ILE A 22 SHEET 6 A 6 GLY A 63 PRO A 66 -1 N HIS A 65 O LEU A 74 SHEET 1 B 8 LYS A 203 ARG A 208 0 SHEET 2 B 8 ALA A 232 HIS A 238 -1 O VAL A 235 N THR A 205 SHEET 3 B 8 THR A 297 ASN A 307 -1 O LEU A 302 N VAL A 234 SHEET 4 B 8 HIS A 246 ASP A 257 1 N LEU A 249 O HIS A 299 SHEET 5 B 8 THR A 356 ALA A 361 1 O PHE A 358 N VAL A 250 SHEET 6 B 8 ARG A 452 ASP A 457 1 O ARG A 452 N ILE A 357 SHEET 7 B 8 GLY A 376 THR A 380 -1 N MET A 379 O HIS A 455 SHEET 8 B 8 VAL A 400 PRO A 402 1 O ALA A 401 N ALA A 378 SHEET 1 C 3 ILE A 319 LYS A 321 0 SHEET 2 C 3 THR A 327 GLU A 329 -1 O VAL A 328 N ILE A 320 SHEET 3 C 3 MET A 421 LYS A 422 1 O MET A 421 N GLU A 329 SHEET 1 D 2 GLU A 463 VAL A 464 0 SHEET 2 D 2 ARG A 467 GLY A 468 -1 O ARG A 467 N VAL A 464 LINK NZ LYS A 252 ZN ZN A 702 1555 1555 2.12 LINK OD2 ASP A 257 ZN ZN A 701 1555 1555 2.05 LINK OD2 ASP A 257 ZN ZN A 702 1555 1555 2.58 LINK OD2 ASP A 275 ZN ZN A 702 1555 1555 1.97 LINK O ASP A 334 ZN ZN A 701 1555 1555 2.19 LINK OD1 ASP A 334 ZN ZN A 701 1555 1555 1.99 LINK OE2 GLU A 336 ZN ZN A 701 1555 1555 2.04 LINK OE1 GLU A 336 ZN ZN A 702 1555 1555 2.06 LINK ZN ZN A 701 O HOH A2159 1555 1555 2.03 LINK ZN ZN A 702 O HOH A2159 1555 1555 2.09 LINK O4 SO4 A 902 NA NA A2001 1555 1555 2.30 SITE 1 AC1 6 ASP A 257 ASP A 334 GLU A 336 ZN A 702 SITE 2 AC1 6 GOL A1003 HOH A2159 SITE 1 AC2 7 LYS A 252 ASP A 257 ASP A 275 GLU A 336 SITE 2 AC2 7 ZN A 701 BCT A 801 HOH A2159 SITE 1 AC3 9 LYS A 252 ALA A 335 GLU A 336 GLY A 337 SITE 2 AC3 9 ARG A 338 LEU A 363 ZN A 702 GOL A1002 SITE 3 AC3 9 HOH A2159 SITE 1 AC4 5 LYS A 98 ARG A 467 HOH A2482 HOH A2534 SITE 2 AC4 5 HOH A2622 SITE 1 AC5 4 SER A 139 GLY A 140 ARG A 142 NA A2001 SITE 1 AC6 1 SO4 A 902 SITE 1 AC7 8 LYS A 326 MET A 421 ALA A 443 PHE A 447 SITE 2 AC7 8 HOH A2555 HOH A2619 HOH A2637 HOH A2657 SITE 1 AC8 10 LYS A 266 ASN A 332 ASP A 334 THR A 364 SITE 2 AC8 10 GLY A 365 BCT A 801 GOL A1003 GOL A1015 SITE 3 AC8 10 HOH A2043 HOH A2460 SITE 1 AC9 13 ASP A 257 LYS A 264 MET A 272 ASP A 275 SITE 2 AC9 13 THR A 362 LEU A 363 THR A 364 GLY A 365 SITE 3 AC9 13 ZN A 701 GOL A1002 HOH A2036 HOH A2159 SITE 4 AC9 13 HOH A2396 SITE 1 BC1 6 LEU A 385 GLU A 388 ARG A 452 LEU A 479 SITE 2 BC1 6 LEU A 480 TYR A 483 SITE 1 BC2 8 PHE A 114 ALA A 115 GLU A 116 VAL A 151 SITE 2 BC2 8 CYS A 152 ASP A 153 GOL A1011 HOH A2294 SITE 1 BC3 8 LYS A 25 GLU A 116 PRO A 118 ASP A 119 SITE 2 BC3 8 HOH A2225 HOH A2293 HOH A2380 HOH A2616 SITE 1 BC4 5 THR A 156 ASN A 157 GLU A 158 HOH A2311 SITE 2 BC4 5 HOH A2443 SITE 1 BC5 3 GLY A 36 LYS A 39 HOH A2461 SITE 1 BC6 9 ARG A 7 ALA A 12 VAL A 13 GLY A 14 SITE 2 BC6 9 ASN A 145 ASN A 147 GOL A1014 HOH A2175 SITE 3 BC6 9 HOH A2452 SITE 1 BC7 10 ARG A 373 ASP A 430 GLU A 463 VAL A 464 SITE 2 BC7 10 GLY A 465 HOH A2063 HOH A2176 HOH A2208 SITE 3 BC7 10 HOH A2226 HOH A2429 SITE 1 BC8 7 GLU A 116 TYR A 117 CYS A 152 ASP A 153 SITE 2 BC8 7 LYS A 154 GOL A1005 HOH A2383 SITE 1 BC9 6 ASP A 187 ASP A 191 ARG A 208 GOL A1014 SITE 2 BC9 6 HOH A2423 HOH A2426 SITE 1 CC1 6 GLN A 11 ALA A 12 LYS A 37 HOH A2330 SITE 2 CC1 6 HOH A2600 HOH A2659 SITE 1 CC2 8 ASP A 191 VAL A 194 LYS A 195 GOL A1009 SITE 2 CC2 8 GOL A1012 HOH A2089 HOH A2213 HOH A2305 SITE 1 CC3 9 ASN A 332 ARG A 338 ALA A 366 SER A 424 SITE 2 CC3 9 PRO A 433 GOL A1002 HOH A2043 HOH A2209 SITE 3 CC3 9 HOH A2234 SITE 1 CC4 5 THR A 138 SER A 324 LYS A 326 HOH A2118 SITE 2 CC4 5 HOH A2526 CRYST1 131.309 131.309 126.344 90.00 90.00 120.00 P 63 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 0.007616 0.004397 0.000000 0.00000 SCALE2 0.000000 0.008794 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007915 0.00000