HEADER HYDROLASE 03-SEP-08 3EDY TITLE CRYSTAL STRUCTURE OF THE PRECURSOR FORM OF HUMAN TRIPEPTIDYL-PEPTIDASE TITLE 2 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIPEPTIDYL-PEPTIDASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 20-563; COMPND 5 SYNONYM: TRIPEPTIDYL-PEPTIDASE I, TPP-1, TPP-I, TRIPEPTIDYL COMPND 6 AMINOPEPTIDASE, LYSOSOMAL PEPSTATIN- INSENSITIVE PROTEASE, LPIC, CELL COMPND 7 GROWTH-INHIBITING GENE 1 PROTEIN; COMPND 8 EC: 3.4.14.9; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TPP1, CLN2; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 9 EXPRESSION_SYSTEM_CELL: OVARY CELLS KEYWDS PROTEASE, TPP1, SEDOLISIN, BATTEN DISEASE, LINCL, ZYMOGEN, PRODOMAIN, KEYWDS 2 EXOPEPTIDASE, ENDOPEPTIDASE, S53 FAMILY, CLN2, CATALYTIC TRIAD, KEYWDS 3 OXYANION HOLE, DISEASE MUTATION, EPILEPSY, GLYCOPROTEIN, HYDROLASE, KEYWDS 4 LYSOSOME, NEURONAL CEROID LIPOFUSCINOSIS, SERINE PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR J.GUHANIYOGI,I.SOHAR,K.DAS,P.LOBEL,A.M.STOCK REVDAT 5 29-JUL-20 3EDY 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 25-OCT-17 3EDY 1 REMARK REVDAT 3 13-JUL-11 3EDY 1 VERSN REVDAT 2 17-FEB-09 3EDY 1 VERSN JRNL REVDAT 1 18-NOV-08 3EDY 0 JRNL AUTH J.GUHANIYOGI,I.SOHAR,K.DAS,A.M.STOCK,P.LOBEL JRNL TITL CRYSTAL STRUCTURE AND AUTOACTIVATION PATHWAY OF THE JRNL TITL 2 PRECURSOR FORM OF HUMAN TRIPEPTIDYL-PEPTIDASE 1, THE ENZYME JRNL TITL 3 DEFICIENT IN LATE INFANTILE CEROID LIPOFUSCINOSIS JRNL REF J.BIOL.CHEM. V. 284 3985 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19038967 JRNL DOI 10.1074/JBC.M806943200 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 29.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 48127 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1231 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) : 2319 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.1930 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.2400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4195 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 73 REMARK 3 SOLVENT ATOMS : 235 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 37.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : 0.13000 REMARK 3 B33 (A**2) : -0.10000 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): 0.134 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.120 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.220 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4428 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2987 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6046 ; 1.263 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7204 ; 1.038 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 543 ; 7.328 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 200 ;36.405 ;23.300 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 638 ;13.894 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;15.069 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 656 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4948 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 912 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 910 ; 0.226 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3163 ; 0.227 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2189 ; 0.191 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2223 ; 0.106 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 234 ; 0.146 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.135 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 16 ; 0.188 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 63 ; 0.291 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.109 ; 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): 2788 ; 1.466 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1093 ; 0.462 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4395 ; 2.165 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1870 ; 3.351 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1651 ; 4.871 ; 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 : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 20 A 183 REMARK 3 ORIGIN FOR THE GROUP (A): 66.2738 -13.0538 2.1520 REMARK 3 T TENSOR REMARK 3 T11: 0.1090 T22: -0.0184 REMARK 3 T33: 0.0690 T12: 0.0046 REMARK 3 T13: 0.0230 T23: 0.0418 REMARK 3 L TENSOR REMARK 3 L11: 0.5650 L22: 0.4290 REMARK 3 L33: 2.4410 L12: 0.1373 REMARK 3 L13: 0.3702 L23: 0.3489 REMARK 3 S TENSOR REMARK 3 S11: 0.0294 S12: 0.0164 S13: -0.1074 REMARK 3 S21: 0.0235 S22: -0.0523 S23: -0.0371 REMARK 3 S31: 0.3268 S32: -0.0087 S33: 0.0229 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 184 A 197 REMARK 3 ORIGIN FOR THE GROUP (A): 62.6178 31.8842 -3.9333 REMARK 3 T TENSOR REMARK 3 T11: 0.1573 T22: 0.0908 REMARK 3 T33: 0.1681 T12: -0.0775 REMARK 3 T13: -0.0203 T23: 0.0363 REMARK 3 L TENSOR REMARK 3 L11: 6.3336 L22: 6.8069 REMARK 3 L33: 6.1013 L12: -0.6618 REMARK 3 L13: 0.4216 L23: -6.4409 REMARK 3 S TENSOR REMARK 3 S11: -0.0083 S12: -0.2337 S13: 0.5860 REMARK 3 S21: 1.3167 S22: -0.3865 S23: -0.3336 REMARK 3 S31: -0.9541 S32: 0.6932 S33: 0.3947 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 198 A 292 REMARK 3 ORIGIN FOR THE GROUP (A): 78.2416 15.3592 5.4954 REMARK 3 T TENSOR REMARK 3 T11: 0.0480 T22: 0.0869 REMARK 3 T33: 0.0993 T12: -0.0017 REMARK 3 T13: 0.0054 T23: 0.0342 REMARK 3 L TENSOR REMARK 3 L11: 1.4037 L22: 1.6964 REMARK 3 L33: 1.5827 L12: 0.1583 REMARK 3 L13: -0.1315 L23: -0.3295 REMARK 3 S TENSOR REMARK 3 S11: 0.0123 S12: 0.0931 S13: -0.0044 REMARK 3 S21: -0.0877 S22: -0.0353 S23: -0.1322 REMARK 3 S31: 0.0029 S32: 0.1054 S33: 0.0230 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 293 A 401 REMARK 3 ORIGIN FOR THE GROUP (A): 63.3730 2.6706 8.3560 REMARK 3 T TENSOR REMARK 3 T11: 0.0762 T22: 0.0683 REMARK 3 T33: 0.0576 T12: 0.0004 REMARK 3 T13: 0.0202 T23: 0.0432 REMARK 3 L TENSOR REMARK 3 L11: 1.5278 L22: 1.1679 REMARK 3 L33: 1.0363 L12: -0.1039 REMARK 3 L13: 0.1647 L23: -0.0415 REMARK 3 S TENSOR REMARK 3 S11: 0.0340 S12: 0.0259 S13: 0.0340 REMARK 3 S21: -0.0423 S22: -0.0643 S23: -0.0200 REMARK 3 S31: 0.0100 S32: -0.0206 S33: 0.0303 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 402 A 563 REMARK 3 ORIGIN FOR THE GROUP (A): 60.1360 12.7024 16.8630 REMARK 3 T TENSOR REMARK 3 T11: 0.0682 T22: 0.0989 REMARK 3 T33: 0.0534 T12: 0.0086 REMARK 3 T13: 0.0273 T23: 0.0171 REMARK 3 L TENSOR REMARK 3 L11: 0.8905 L22: 0.5261 REMARK 3 L33: 0.3547 L12: 0.1013 REMARK 3 L13: 0.0795 L23: -0.0848 REMARK 3 S TENSOR REMARK 3 S11: 0.0297 S12: -0.1673 S13: 0.0512 REMARK 3 S21: 0.0851 S22: -0.0316 S23: 0.0229 REMARK 3 S31: -0.0269 S32: -0.0671 S33: 0.0019 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 3EDY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1000049202. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97908 REMARK 200 MONOCHROMATOR : HORIZONTALLY DEFLECTING AND REMARK 200 FOCUSING CRYSTAL PRECEDED BY A REMARK 200 VERTICALLY FOCUSING MIRROR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50890 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.45700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, CITRATE, PH 5.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 29.90350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.23950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.58650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.23950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.90350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.58650 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: 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 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 174 -55.50 -142.74 REMARK 500 HIS A 197 112.85 -169.11 REMARK 500 GLU A 232 70.70 -66.02 REMARK 500 SER A 293 89.95 -167.01 REMARK 500 SER A 294 61.61 -115.76 REMARK 500 PRO A 295 -178.84 -55.99 REMARK 500 HIS A 298 78.95 -151.58 REMARK 500 ILE A 399 32.80 -93.99 REMARK 500 THR A 400 -150.65 -79.17 REMARK 500 VAL A 415 -53.19 -122.57 REMARK 500 SER A 525 -156.62 -155.04 REMARK 500 PRO A 544 32.09 -87.77 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 VAL A 190 THR A 191 145.34 REMARK 500 PHE A 397 LEU A 398 -146.56 REMARK 500 REMARK 500 REMARK: NULL DBREF 3EDY A 20 563 UNP O14773 TPP1_HUMAN 20 563 SEQRES 1 A 544 SER TYR SER PRO GLU PRO ASP GLN ARG ARG THR LEU PRO SEQRES 2 A 544 PRO GLY TRP VAL SER LEU GLY ARG ALA ASP PRO GLU GLU SEQRES 3 A 544 GLU LEU SER LEU THR PHE ALA LEU ARG GLN GLN ASN VAL SEQRES 4 A 544 GLU ARG LEU SER GLU LEU VAL GLN ALA VAL SER ASP PRO SEQRES 5 A 544 SER SER PRO GLN TYR GLY LYS TYR LEU THR LEU GLU ASN SEQRES 6 A 544 VAL ALA ASP LEU VAL ARG PRO SER PRO LEU THR LEU HIS SEQRES 7 A 544 THR VAL GLN LYS TRP LEU LEU ALA ALA GLY ALA GLN LYS SEQRES 8 A 544 CYS HIS SER VAL ILE THR GLN ASP PHE LEU THR CYS TRP SEQRES 9 A 544 LEU SER ILE ARG GLN ALA GLU LEU LEU LEU PRO GLY ALA SEQRES 10 A 544 GLU PHE HIS HIS TYR VAL GLY GLY PRO THR GLU THR HIS SEQRES 11 A 544 VAL VAL ARG SER PRO HIS PRO TYR GLN LEU PRO GLN ALA SEQRES 12 A 544 LEU ALA PRO HIS VAL ASP PHE VAL GLY GLY LEU HIS ARG SEQRES 13 A 544 PHE PRO PRO THR SER SER LEU ARG GLN ARG PRO GLU PRO SEQRES 14 A 544 GLN VAL THR GLY THR VAL GLY LEU HIS LEU GLY VAL THR SEQRES 15 A 544 PRO SER VAL ILE ARG LYS ARG TYR ASN LEU THR SER GLN SEQRES 16 A 544 ASP VAL GLY SER GLY THR SER ASN ASN SER GLN ALA CYS SEQRES 17 A 544 ALA GLN PHE LEU GLU GLN TYR PHE HIS ASP SER ASP LEU SEQRES 18 A 544 ALA GLN PHE MET ARG LEU PHE GLY GLY ASN PHE ALA HIS SEQRES 19 A 544 GLN ALA SER VAL ALA ARG VAL VAL GLY GLN GLN GLY ARG SEQRES 20 A 544 GLY ARG ALA GLY ILE GLU ALA SER LEU ASP VAL GLN TYR SEQRES 21 A 544 LEU MET SER ALA GLY ALA ASN ILE SER THR TRP VAL TYR SEQRES 22 A 544 SER SER PRO GLY ARG HIS GLU GLY GLN GLU PRO PHE LEU SEQRES 23 A 544 GLN TRP LEU MET LEU LEU SER ASN GLU SER ALA LEU PRO SEQRES 24 A 544 HIS VAL HIS THR VAL SER TYR GLY ASP ASP GLU ASP SER SEQRES 25 A 544 LEU SER SER ALA TYR ILE GLN ARG VAL ASN THR GLU LEU SEQRES 26 A 544 MET LYS ALA ALA ALA ARG GLY LEU THR LEU LEU PHE ALA SEQRES 27 A 544 SER GLY ASP SER GLY ALA GLY CYS TRP SER VAL SER GLY SEQRES 28 A 544 ARG HIS GLN PHE ARG PRO THR PHE PRO ALA SER SER PRO SEQRES 29 A 544 TYR VAL THR THR VAL GLY GLY THR SER PHE GLN GLU PRO SEQRES 30 A 544 PHE LEU ILE THR ASN GLU ILE VAL ASP TYR ILE SER GLY SEQRES 31 A 544 GLY GLY PHE SER ASN VAL PHE PRO ARG PRO SER TYR GLN SEQRES 32 A 544 GLU GLU ALA VAL THR LYS PHE LEU SER SER SER PRO HIS SEQRES 33 A 544 LEU PRO PRO SER SER TYR PHE ASN ALA SER GLY ARG ALA SEQRES 34 A 544 TYR PRO ASP VAL ALA ALA LEU SER ASP GLY TYR TRP VAL SEQRES 35 A 544 VAL SER ASN ARG VAL PRO ILE PRO TRP VAL SER GLY THR SEQRES 36 A 544 SER ALA SER THR PRO VAL PHE GLY GLY ILE LEU SER LEU SEQRES 37 A 544 ILE ASN GLU HIS ARG ILE LEU SER GLY ARG PRO PRO LEU SEQRES 38 A 544 GLY PHE LEU ASN PRO ARG LEU TYR GLN GLN HIS GLY ALA SEQRES 39 A 544 GLY LEU PHE ASP VAL THR ARG GLY CYS HIS GLU SER CYS SEQRES 40 A 544 LEU ASP GLU GLU VAL GLU GLY GLN GLY PHE CYS SER GLY SEQRES 41 A 544 PRO GLY TRP ASP PRO VAL THR GLY TRP GLY THR PRO ASN SEQRES 42 A 544 PHE PRO ALA LEU LEU LYS THR LEU LEU ASN PRO MODRES 3EDY ASN A 210 ASN GLYCOSYLATION SITE MODRES 3EDY ASN A 286 ASN GLYCOSYLATION SITE MODRES 3EDY ASN A 313 ASN GLYCOSYLATION SITE MODRES 3EDY ASN A 443 ASN GLYCOSYLATION SITE HET CA A 1 1 HET NAG A 564 14 HET NAG A 565 14 HET NAG A 566 14 HET NAG A 567 14 HET EDO A 701 4 HET EDO A 702 4 HET EDO A 703 4 HET EDO A 704 4 HETNAM CA CALCIUM ION HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 CA CA 2+ FORMUL 3 NAG 4(C8 H15 N O6) FORMUL 7 EDO 4(C2 H6 O2) FORMUL 11 HOH *235(H2 O) HELIX 1 1 ASN A 57 ASP A 70 1 14 HELIX 2 2 THR A 81 ARG A 90 1 10 HELIX 3 3 SER A 92 GLY A 107 1 16 HELIX 4 4 ILE A 126 LEU A 133 1 8 HELIX 5 5 PRO A 160 ALA A 164 5 5 HELIX 6 6 THR A 201 TYR A 209 1 9 HELIX 7 7 HIS A 236 GLY A 248 1 13 HELIX 8 8 GLY A 270 GLY A 284 1 15 HELIX 9 9 GLU A 302 SER A 312 1 11 HELIX 10 10 ASP A 330 LEU A 332 5 3 HELIX 11 11 SER A 333 ARG A 350 1 18 HELIX 12 12 PRO A 419 TYR A 421 5 3 HELIX 13 13 GLN A 422 SER A 433 1 12 HELIX 14 14 PRO A 438 PHE A 442 5 5 HELIX 15 15 GLY A 473 SER A 495 1 23 HELIX 16 16 LEU A 503 GLN A 510 1 8 HELIX 17 17 ASN A 552 THR A 559 1 8 SHEET 1 A 3 TRP A 35 ARG A 40 0 SHEET 2 A 3 HIS A 139 GLY A 143 -1 O HIS A 140 N LEU A 38 SHEET 3 A 3 THR A 148 ARG A 152 -1 O ARG A 152 N HIS A 139 SHEET 1 B 4 GLN A 109 SER A 113 0 SHEET 2 B 4 PHE A 119 SER A 125 -1 O TRP A 123 N GLN A 109 SHEET 3 B 4 GLU A 46 LEU A 53 -1 N LEU A 47 O LEU A 124 SHEET 4 B 4 VAL A 167 VAL A 170 -1 O ASP A 168 N ALA A 52 SHEET 1 C 7 ARG A 259 VAL A 261 0 SHEET 2 C 7 SER A 288 TYR A 292 1 O VAL A 291 N VAL A 261 SHEET 3 C 7 SER A 224 GLN A 229 1 N GLN A 225 O TRP A 290 SHEET 4 C 7 VAL A 320 SER A 324 1 O THR A 322 N ALA A 226 SHEET 5 C 7 THR A 353 ALA A 357 1 O LEU A 355 N VAL A 323 SHEET 6 C 7 THR A 386 PHE A 393 1 O VAL A 388 N PHE A 356 SHEET 7 C 7 GLU A 402 VAL A 404 -1 O ILE A 403 N SER A 392 SHEET 1 D 7 ARG A 259 VAL A 261 0 SHEET 2 D 7 SER A 288 TYR A 292 1 O VAL A 291 N VAL A 261 SHEET 3 D 7 SER A 224 GLN A 229 1 N GLN A 225 O TRP A 290 SHEET 4 D 7 VAL A 320 SER A 324 1 O THR A 322 N ALA A 226 SHEET 5 D 7 THR A 353 ALA A 357 1 O LEU A 355 N VAL A 323 SHEET 6 D 7 THR A 386 PHE A 393 1 O VAL A 388 N PHE A 356 SHEET 7 D 7 VAL A 452 LEU A 455 1 O VAL A 452 N GLY A 389 SHEET 1 E 2 ASP A 327 ASP A 328 0 SHEET 2 E 2 THR A 377 PHE A 378 -1 O PHE A 378 N ASP A 327 SHEET 1 F 2 TRP A 366 VAL A 368 0 SHEET 2 F 2 ARG A 371 GLN A 373 -1 O ARG A 371 N VAL A 368 SHEET 1 G 2 GLY A 411 PRO A 417 0 SHEET 2 G 2 GLY A 446 TYR A 449 -1 O ARG A 447 N PHE A 416 SHEET 1 H 2 TYR A 459 SER A 463 0 SHEET 2 H 2 VAL A 466 VAL A 471 -1 O ILE A 468 N VAL A 461 SHEET 1 I 2 LEU A 515 PHE A 516 0 SHEET 2 I 2 THR A 550 PRO A 551 -1 O THR A 550 N PHE A 516 SHEET 1 J 2 CYS A 522 GLU A 524 0 SHEET 2 J 2 GLN A 534 CYS A 537 -1 O GLY A 535 N HIS A 523 SSBOND 1 CYS A 111 CYS A 122 1555 1555 2.07 SSBOND 2 CYS A 365 CYS A 526 1555 1555 2.09 SSBOND 3 CYS A 522 CYS A 537 1555 1555 2.07 LINK ND2 ASN A 210 C1 NAG A 564 1555 1555 1.60 LINK ND2 ASN A 286 C1 NAG A 565 1555 1555 1.44 LINK ND2 ASN A 313 C1 NAG A 566 1555 1555 1.55 LINK ND2 ASN A 443 C1 NAG A 567 1555 1555 1.46 CISPEP 1 PHE A 378 PRO A 379 0 8.61 CISPEP 2 TYR A 449 PRO A 450 0 24.78 CISPEP 3 ASN A 562 PRO A 563 0 0.77 CRYST1 59.807 93.173 102.479 90.00 90.00 90.00 P 21 21 21 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 0.016720 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009758 0.00000