HEADER HYDROLASE/HYDROLASE INHIBITOR 13-APR-16 5JBT TITLE MESOTRYPSIN IN COMPLEX WITH CLEAVED AMYLOID PRECURSOR LIKE PROTEIN 2 TITLE 2 INHIBITOR (APLP2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRSS3 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: AMYLOID-LIKE PROTEIN 2; COMPND 8 CHAIN: X; COMPND 9 SYNONYM: APLP-2,APPH,AMYLOID PROTEIN HOMOLOG,CDEI BOX-BINDING COMPND 10 PROTEIN,CDEBP; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: AMYLOID-LIKE PROTEIN 2; COMPND 14 CHAIN: Y; COMPND 15 SYNONYM: APLP-2,APPH,AMYLOID PROTEIN HOMOLOG,CDEI BOX-BINDING COMPND 16 PROTEIN,CDEBP; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: PANCREAS; SOURCE 6 GENE: PRSS3; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTRAP-T7-WTHU3; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: APLP2, APPL2; SOURCE 16 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PPICZA; SOURCE 19 MOL_ID: 3; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_COMMON: HUMAN; SOURCE 22 ORGANISM_TAXID: 9606; SOURCE 23 GENE: APLP2, APPL2; SOURCE 24 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 25 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 26 EXPRESSION_SYSTEM_PLASMID: PPICZA KEYWDS INHIBITOR PROTEASE SERINE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR O.KAYODE,R.WANG,D.PENDLEBURY,A.SOARES,E.S.RADISKY REVDAT 6 27-SEP-23 5JBT 1 REMARK REVDAT 5 04-DEC-19 5JBT 1 REMARK REVDAT 4 06-SEP-17 5JBT 1 REMARK REVDAT 3 28-DEC-16 5JBT 1 JRNL REVDAT 2 16-NOV-16 5JBT 1 REMARK REVDAT 1 09-NOV-16 5JBT 0 JRNL AUTH O.KAYODE,R.WANG,D.F.PENDLEBURY,I.COHEN,R.D.HENIN,A.HOCKLA, JRNL AUTH 2 A.S.SOARES,N.PAPO,T.R.CAULFIELD,E.S.RADISKY JRNL TITL AN ACROBATIC SUBSTRATE METAMORPHOSIS REVEALS A REQUIREMENT JRNL TITL 2 FOR SUBSTRATE CONFORMATIONAL DYNAMICS IN TRYPSIN JRNL TITL 3 PROTEOLYSIS. JRNL REF J. BIOL. CHEM. V. 291 26304 2016 JRNL REFN ESSN 1083-351X JRNL PMID 27810896 JRNL DOI 10.1074/JBC.M116.758417 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 57667 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3082 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.43 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4067 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 218 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2096 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 259 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.03000 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): 0.060 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.058 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.508 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2180 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2022 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2968 ; 2.156 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4643 ; 2.303 ; 3.007 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 281 ; 6.463 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;34.389 ;24.194 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 349 ;11.453 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;20.342 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 318 ; 0.147 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2522 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 504 ; 0.016 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 4202 ; 7.104 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 85 ;31.238 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4322 ;12.908 ; 5.000 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5JBT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000211083. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57667 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.398 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.23100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.760 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3L33 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE 0.1 M SODIUM REMARK 280 CACODYLATE TRIHYDRATE 30% PEG 8000, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 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 49.47800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.26950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.47800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.26950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, X, Y 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 Y 206 LIES ON A SPECIAL POSITION. REMARK 375 HOH Y 210 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET Y 18 CG SD CE REMARK 470 TYR Y 35 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN Y 44 OD1 ND2 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 HOH A 491 O HOH A 498 1.98 REMARK 500 O HOH Y 219 O HOH Y 221 2.07 REMARK 500 O HOH A 491 O HOH A 614 2.17 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 SER A 37 CB SER A 37 OG 0.097 REMARK 500 GLU A 186 CD GLU A 186 OE1 0.078 REMARK 500 PRO Y 19 C PRO Y 19 O -0.147 REMARK 500 ASP Y 49 CG ASP Y 49 OD1 0.169 REMARK 500 CYS Y 51 CB CYS Y 51 SG -0.111 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 MET A 104 CA - CB - CG ANGL. DEV. = 11.1 DEGREES REMARK 500 LYS A 188 CG - CD - CE ANGL. DEV. = 18.2 DEGREES REMARK 500 LYS A 188 CD - CE - NZ ANGL. DEV. = -16.4 DEGREES REMARK 500 ASP A 189 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 189 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 224 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG Y 32 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG Y 42 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ASP Y 49 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP Y 49 CB - CG - OD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 CYS Y 51 CA - CB - SG ANGL. DEV. = 11.5 DEGREES REMARK 500 MET Y 52 CG - SD - CE ANGL. DEV. = 11.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 71 -67.74 -122.67 REMARK 500 ARG A 193 8.41 80.86 REMARK 500 SER A 214 -69.75 -125.74 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 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 70 OE2 REMARK 620 2 ASN A 72 O 88.0 REMARK 620 3 VAL A 75 O 162.1 85.0 REMARK 620 4 GLU A 77 OE1 103.5 98.1 93.8 REMARK 620 5 GLU A 80 OE2 100.3 165.9 90.0 68.9 REMARK 620 6 HOH A 463 O 80.4 102.3 85.0 159.3 90.4 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 CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 Y 101 DBREF 5JBT A 16 246 UNP Q8N2U3 Q8N2U3_HUMAN 28 251 DBREF 5JBT X 2 15 UNP Q06481 APLP2_HUMAN 307 320 DBREF 5JBT Y 18 55 UNP Q06481 APLP2_HUMAN 323 360 SEQADV 5JBT ALA A 195 UNP Q8N2U3 SER 204 ENGINEERED MUTATION SEQRES 1 A 224 ILE VAL GLY GLY TYR THR CYS GLU GLU ASN SER LEU PRO SEQRES 2 A 224 TYR GLN VAL SER LEU ASN SER GLY SER HIS PHE CYS GLY SEQRES 3 A 224 GLY SER LEU ILE SER GLU GLN TRP VAL VAL SER ALA ALA SEQRES 4 A 224 HIS CYS TYR LYS THR ARG ILE GLN VAL ARG LEU GLY GLU SEQRES 5 A 224 HIS ASN ILE LYS VAL LEU GLU GLY ASN GLU GLN PHE ILE SEQRES 6 A 224 ASN ALA ALA LYS ILE ILE ARG HIS PRO LYS TYR ASN ARG SEQRES 7 A 224 ASP THR LEU ASP ASN ASP ILE MET LEU ILE LYS LEU SER SEQRES 8 A 224 SER PRO ALA VAL ILE ASN ALA ARG VAL SER THR ILE SER SEQRES 9 A 224 LEU PRO THR ALA PRO PRO ALA ALA GLY THR GLU CYS LEU SEQRES 10 A 224 ILE SER GLY TRP GLY ASN THR LEU SER PHE GLY ALA ASP SEQRES 11 A 224 TYR PRO ASP GLU LEU LYS CYS LEU ASP ALA PRO VAL LEU SEQRES 12 A 224 THR GLN ALA GLU CYS LYS ALA SER TYR PRO GLY LYS ILE SEQRES 13 A 224 THR ASN SER MET PHE CYS VAL GLY PHE LEU GLU GLY GLY SEQRES 14 A 224 LYS ASP SER CYS GLN ARG ASP ALA GLY GLY PRO VAL VAL SEQRES 15 A 224 CYS ASN GLY GLN LEU GLN GLY VAL VAL SER TRP GLY HIS SEQRES 16 A 224 GLY CYS ALA TRP LYS ASN ARG PRO GLY VAL TYR THR LYS SEQRES 17 A 224 VAL TYR ASN TYR VAL ASP TRP ILE LYS ASP THR ILE ALA SEQRES 18 A 224 ALA ASN SER SEQRES 1 X 14 LYS ALA VAL CYS SER GLN GLU ALA MET THR GLY PRO CYS SEQRES 2 X 14 ARG SEQRES 1 Y 38 MET PRO ARG TRP TYR PHE ASP LEU SER LYS GLY LYS CYS SEQRES 2 Y 38 VAL ARG PHE ILE TYR GLY GLY CYS GLY GLY ASN ARG ASN SEQRES 3 Y 38 ASN PHE GLU SER GLU ASP TYR CYS MET ALA VAL CYS HET CA A 301 1 HET SO4 Y 101 5 HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION FORMUL 4 CA CA 2+ FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *259(H2 O) HELIX 1 AA1 ALA A 55 TYR A 59 5 5 HELIX 2 AA2 THR A 164 TYR A 172 1 9 HELIX 3 AA3 TYR A 234 ASN A 245 1 12 HELIX 4 AA4 GLY Y 39 ASN Y 43 5 5 HELIX 5 AA5 SER Y 47 CYS Y 55 1 9 SHEET 1 AA1 7 TYR A 20 THR A 21 0 SHEET 2 AA1 7 LYS A 156 PRO A 161 -1 O CYS A 157 N TYR A 20 SHEET 3 AA1 7 GLU A 135 GLY A 140 -1 N ILE A 138 O LEU A 158 SHEET 4 AA1 7 PRO A 198 CYS A 201 -1 O VAL A 200 N LEU A 137 SHEET 5 AA1 7 GLN A 204 TRP A 215 -1 O GLN A 204 N CYS A 201 SHEET 6 AA1 7 GLY A 226 LYS A 230 -1 O VAL A 227 N TRP A 215 SHEET 7 AA1 7 MET A 180 VAL A 183 -1 N PHE A 181 O TYR A 228 SHEET 1 AA2 7 GLN A 30 ASN A 34 0 SHEET 2 AA2 7 HIS A 40 SER A 48 -1 O CYS A 42 N LEU A 33 SHEET 3 AA2 7 TRP A 51 SER A 54 -1 O VAL A 53 N SER A 45 SHEET 4 AA2 7 MET A 104 LEU A 108 -1 O ILE A 106 N VAL A 52 SHEET 5 AA2 7 GLN A 81 ARG A 90 -1 N ILE A 89 O LEU A 105 SHEET 6 AA2 7 GLN A 64 LEU A 67 -1 N VAL A 65 O ILE A 83 SHEET 7 AA2 7 GLN A 30 ASN A 34 -1 N SER A 32 O ARG A 66 SHEET 1 AA3 2 ARG Y 20 ASP Y 24 0 SHEET 2 AA3 2 LYS Y 29 PHE Y 33 -1 O PHE Y 33 N ARG Y 20 SSBOND 1 CYS A 22 CYS A 157 1555 1555 2.03 SSBOND 2 CYS A 42 CYS A 58 1555 1555 2.09 SSBOND 3 CYS A 136 CYS A 201 1555 1555 2.04 SSBOND 4 CYS A 168 CYS A 182 1555 1555 2.11 SSBOND 5 CYS A 191 CYS A 220 1555 1555 2.08 SSBOND 6 CYS X 5 CYS Y 55 1555 1555 2.07 SSBOND 7 CYS X 14 CYS Y 38 1555 1555 2.08 SSBOND 8 CYS Y 30 CYS Y 51 1555 1555 2.09 LINK OE2 GLU A 70 CA CA A 301 1555 1555 2.29 LINK O ASN A 72 CA CA A 301 1555 1555 2.33 LINK O VAL A 75 CA CA A 301 1555 1555 2.32 LINK OE1 GLU A 77 CA CA A 301 1555 1555 2.52 LINK OE2 GLU A 80 CA CA A 301 1555 1555 2.32 LINK CA CA A 301 O HOH A 463 1555 1555 2.24 SITE 1 AC1 6 GLU A 70 ASN A 72 VAL A 75 GLU A 77 SITE 2 AC1 6 GLU A 80 HOH A 463 SITE 1 AC2 9 HIS A 217 GLY A 219 GLY X 12 PRO X 13 SITE 2 AC2 9 ARG Y 42 ASN Y 43 ASN Y 44 HOH Y 202 SITE 3 AC2 9 HOH Y 218 CRYST1 98.956 54.539 56.632 90.00 90.00 90.00 P 21 21 2 4 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 0.010106 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018336 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017658 0.00000