HEADER HYDROLASE 28-OCT-04 1XVM TITLE TRYPSIN FROM FUSARIUM OXYSPORUM- ROOM TEMPERATURE TO ATOMIC RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPSIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.21.4; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SUBSTRATE TRIPEPTIDE GLY-ALA-ARG; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FUSARIUM OXYSPORUM; SOURCE 3 ORGANISM_TAXID: 5507; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: THE PEPTIDE IS CHEMICALLY SYNTHESIZED. KEYWDS ATOMIC RESOLUTION, MOBILITY, ROOM TEMPERATURE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.SCHMIDT,V.S.LAMZIN REVDAT 4 30-OCT-24 1XVM 1 REMARK REVDAT 3 25-OCT-23 1XVM 1 REMARK REVDAT 2 24-FEB-09 1XVM 1 VERSN REVDAT 1 26-JUL-05 1XVM 0 JRNL AUTH A.SCHMIDT,V.S.LAMZIN JRNL TITL EXTRACTION OF FUNCTIONAL MOTION IN TRYPSIN CRYSTAL JRNL TITL 2 STRUCTURES. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 61 1132 2005 JRNL REFN ISSN 0907-4449 JRNL PMID 16041079 JRNL DOI 10.1107/S0907444905016732 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.144 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.144 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 65556 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.133 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 54851 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1571 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1696.6 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1475.2 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 11 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 15420 REMARK 3 NUMBER OF RESTRAINTS : 19268 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.022 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.029 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.081 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.085 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.078 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.041 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.067 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT, HYDROGENS REMARK 3 INCLUDED, REFINEMENT AGAINST DIFFRACTION INTENSITIES REMARK 4 REMARK 4 1XVM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000030815. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8030 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS 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 : 65556 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36100 REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: 1PQ5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM CITRATE, PH REMARK 280 5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 ARG A 88 CG CD NE CZ NH1 NH2 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 OG SER A 195 C ARG B 2003 1.48 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 PHE A 27 CB - CG - CD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 CYS A 41 CA - CB - SG ANGL. DEV. = 11.1 DEGREES REMARK 500 ARG A 69 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 69 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 218 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 232 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B2003 NE - CZ - NH2 ANGL. DEV. = -4.2 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 TRP A 40 -64.01 -146.35 REMARK 500 TRP A 40 -58.48 -146.35 REMARK 500 SER A 211 -66.32 -123.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PQ8 RELATED DB: PDB REMARK 900 RELATED ID: 1PQ5 RELATED DB: PDB REMARK 900 RELATED ID: 1PPZ RELATED DB: PDB REMARK 900 RELATED ID: 1PQA RELATED DB: PDB REMARK 900 RELATED ID: 1XVO RELATED DB: PDB REMARK 900 TRYPSIN FROM FUSARIUM OXYSPORUM AT PH 6 DBREF 1XVM A 16 239 UNP P35049 TRYP_FUSOX 25 248 DBREF 1XVM B 2001 2003 PDB 1XVM 1XVM 2001 2003 SEQRES 1 A 224 ILE VAL GLY GLY THR SER ALA SER ALA GLY ASP PHE PRO SEQRES 2 A 224 PHE ILE VAL SER ILE SER ARG ASN GLY GLY PRO TRP CYS SEQRES 3 A 224 GLY GLY SER LEU LEU ASN ALA ASN THR VAL LEU THR ALA SEQRES 4 A 224 ALA HIS CYS VAL SER GLY TYR ALA GLN SER GLY PHE GLN SEQRES 5 A 224 ILE ARG ALA GLY SER LEU SER ARG THR SER GLY GLY ILE SEQRES 6 A 224 THR SER SER LEU SER SER VAL ARG VAL HIS PRO SER TYR SEQRES 7 A 224 SER GLY ASN ASN ASN ASP LEU ALA ILE LEU LYS LEU SER SEQRES 8 A 224 THR SER ILE PRO SER GLY GLY ASN ILE GLY TYR ALA ARG SEQRES 9 A 224 LEU ALA ALA SER GLY SER ASP PRO VAL ALA GLY SER SER SEQRES 10 A 224 ALA THR VAL ALA GLY TRP GLY ALA THR SER GLU GLY GLY SEQRES 11 A 224 SER SER THR PRO VAL ASN LEU LEU LYS VAL THR VAL PRO SEQRES 12 A 224 ILE VAL SER ARG ALA THR CYS ARG ALA GLN TYR GLY THR SEQRES 13 A 224 SER ALA ILE THR ASN GLN MET PHE CYS ALA GLY VAL SER SEQRES 14 A 224 SER GLY GLY LYS ASP SER CYS GLN GLY ASP SER GLY GLY SEQRES 15 A 224 PRO ILE VAL ASP SER SER ASN THR LEU ILE GLY ALA VAL SEQRES 16 A 224 SER TRP GLY ASN GLY CYS ALA ARG PRO ASN TYR SER GLY SEQRES 17 A 224 VAL TYR ALA SER VAL GLY ALA LEU ARG SER PHE ILE ASP SEQRES 18 A 224 THR TYR ALA SEQRES 1 B 3 GLY ALA ARG FORMUL 3 HOH *131(H2 O) HELIX 1 1 ALA A 54 SER A 59 1 6 HELIX 2 2 ALA A 62 SER A 64 5 3 HELIX 3 3 SER A 161 GLY A 170 1 10 HELIX 4 4 VAL A 228 ALA A 239 1 12 SHEET 1 A 8 THR A 20 SER A 21 0 SHEET 2 A 8 LEU A 153 VAL A 160 -1 O LYS A 154 N THR A 20 SHEET 3 A 8 MET A 178 ALA A 181 -1 O CYS A 180 N VAL A 160 SHEET 4 A 8 GLY A 223 SER A 227 -1 O TYR A 225 N PHE A 179 SHEET 5 A 8 LEU A 206 TRP A 212 -1 N TRP A 212 O VAL A 224 SHEET 6 A 8 PRO A 198 ASP A 201 -1 N ILE A 199 O ILE A 207 SHEET 7 A 8 SER A 132 GLY A 137 -1 N THR A 134 O VAL A 200 SHEET 8 A 8 LEU A 153 VAL A 160 -1 O VAL A 157 N ALA A 133 SHEET 1 B 7 ILE A 80 SER A 82 0 SHEET 2 B 7 PHE A 66 ALA A 70 -1 N ILE A 68 O SER A 82 SHEET 3 B 7 ILE A 30 ARG A 35 -1 N SER A 34 O GLN A 67 SHEET 4 B 7 GLY A 38 ASN A 47 -1 O CYS A 41 N ILE A 33 SHEET 5 B 7 THR A 50 THR A 53 -1 O LEU A 52 N SER A 44 SHEET 6 B 7 ALA A 101 LEU A 105 -1 O LEU A 103 N VAL A 51 SHEET 7 B 7 LEU A 84 VAL A 89 -1 N SER A 85 O LYS A 104 SSBOND 1 CYS A 41 CYS A 57 1555 1555 2.03 SSBOND 2 CYS A 165 CYS A 180 1555 1555 2.03 SSBOND 3 CYS A 191 CYS A 216 1555 1555 2.01 CRYST1 33.277 37.037 40.100 102.22 103.93 102.59 P 1 1 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 0.030051 0.006712 0.009710 0.00000 SCALE2 0.000000 0.027665 0.008033 0.00000 SCALE3 0.000000 0.000000 0.026755 0.00000