10 20 30 40 50 60 70 80 1MTZ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 23-SEP-02 1MTZ
TITLE CRYSTAL STRUCTURE OF THE TRICORN INTERACTING FACTOR F1
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROLINE IMINOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PIP, PROLYL AMINOPEPTIDASE, PAP, TRICORN PROTEASE COMPND 5 INTERACTING FACTOR F1; COMPND 6 EC: 3.4.11.5; COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOPLASMA ACIDOPHILUM; SOURCE 3 ORGANISM_TAXID: 2303; SOURCE 4 GENE: TA0830; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRSET6C
KEYWDS ALPHA-BETA HYDROLASE, CAP DOMAIN, CAGED ACTIVE SITE, PROLYL KEYWDS 2 PEPTIDASE
EXPDTA X-RAY DIFFRACTION
AUTHOR P.GOETTIG,M.GROLL,J.-S.KIM,R.HUBER,H.BRANDSTETTER
REVDAT 3 24-FEB-09 1MTZ 1 VERSN REVDAT 2 13-JAN-04 1MTZ 1 JRNL REMARK REVDAT 1 06-NOV-02 1MTZ 0
JRNL AUTH P.GOETTIG,M.GROLL,J.-S.KIM,R.HUBER,H.BRANDSTETTER JRNL TITL STRUCTURES OF THE TRICORN-INTERACTING JRNL TITL 2 AMINOPEPTIDASE F1 WITH DIFFERENT LIGANDS EXPLAIN JRNL TITL 3 ITS CATALYTIC MECHANISM JRNL REF EMBO J. V. 21 5343 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 12374735 JRNL DOI 10.1093/EMBOJ/CDF552
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.2 REMARK 3 NUMBER OF REFLECTIONS : 22449 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 SET) : 0.199 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2207 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2328 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 179 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.71000 REMARK 3 B22 (A**2) : -0.66000 REMARK 3 B33 (A**2) : -1.05000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : 0.17 REMARK 3 LOW RESOLUTION CUTOFF (A) : 20.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.21 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1MTZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-SEP-02. REMARK 100 THE RCSB ID CODE IS RCSB017177.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : DYNAMICALLY BENDABLE MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23078 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1MT3 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 100 MM HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K
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 27.48050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.13700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.54750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.13700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.48050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.54750 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS THE MONOMER IN THE ASYMMETRIC REMARK 300 UNIT
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 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 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 ASP A 2 REMARK 465 GLN A 3
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 GLU A 4 CG CD OE1 OE2
REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 53 CE NZ REMARK 480 LYS A 92 CD CE NZ REMARK 480 LYS A 98 CD CE NZ REMARK 480 LYS A 157 CG CD CE NZ
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 40 -135.66 -86.26 REMARK 500 SER A 105 -124.62 55.36 REMARK 500 ALA A 150 -50.80 -26.43 REMARK 500 SER A 185 46.28 29.74 REMARK 500 ASN A 209 -69.55 -97.73 REMARK 500 ASP A 224 112.66 -162.33 REMARK 500 ASP A 268 -6.32 67.31 REMARK 500 SER A 270 -134.32 -124.58 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MT3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE TRICORN INTERACTING FACTOR REMARK 900 SELENOMETHIONINE-F1 REMARK 900 RELATED ID: 1MU0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE TRICORN INTERACTING FACTOR F1 REMARK 900 COMPLEX WITH PCK
DBREF 1MTZ A 1 293 UNP P96084 PIP_THEAC 1 293
SEQRES 1 A 293 MET ASP GLN GLU CYS ILE GLU ASN TYR ALA LYS VAL ASN SEQRES 2 A 293 GLY ILE TYR ILE TYR TYR LYS LEU CYS LYS ALA PRO GLU SEQRES 3 A 293 GLU LYS ALA LYS LEU MET THR MET HIS GLY GLY PRO GLY SEQRES 4 A 293 MET SER HIS ASP TYR LEU LEU SER LEU ARG ASP MET THR SEQRES 5 A 293 LYS GLU GLY ILE THR VAL LEU PHE TYR ASP GLN PHE GLY SEQRES 6 A 293 CYS GLY ARG SER GLU GLU PRO ASP GLN SER LYS PHE THR SEQRES 7 A 293 ILE ASP TYR GLY VAL GLU GLU ALA GLU ALA LEU ARG SER SEQRES 8 A 293 LYS LEU PHE GLY ASN GLU LYS VAL PHE LEU MET GLY SER SEQRES 9 A 293 SER TYR GLY GLY ALA LEU ALA LEU ALA TYR ALA VAL LYS SEQRES 10 A 293 TYR GLN ASP HIS LEU LYS GLY LEU ILE VAL SER GLY GLY SEQRES 11 A 293 LEU SER SER VAL PRO LEU THR VAL LYS GLU MET ASN ARG SEQRES 12 A 293 LEU ILE ASP GLU LEU PRO ALA LYS TYR ARG ASP ALA ILE SEQRES 13 A 293 LYS LYS TYR GLY SER SER GLY SER TYR GLU ASN PRO GLU SEQRES 14 A 293 TYR GLN GLU ALA VAL ASN TYR PHE TYR HIS GLN HIS LEU SEQRES 15 A 293 LEU ARG SER GLU ASP TRP PRO PRO GLU VAL LEU LYS SER SEQRES 16 A 293 LEU GLU TYR ALA GLU ARG ARG ASN VAL TYR ARG ILE MET SEQRES 17 A 293 ASN GLY PRO ASN GLU PHE THR ILE THR GLY THR ILE LYS SEQRES 18 A 293 ASP TRP ASP ILE THR ASP LYS ILE SER ALA ILE LYS ILE SEQRES 19 A 293 PRO THR LEU ILE THR VAL GLY GLU TYR ASP GLU VAL THR SEQRES 20 A 293 PRO ASN VAL ALA ARG VAL ILE HIS GLU LYS ILE ALA GLY SEQRES 21 A 293 SER GLU LEU HIS VAL PHE ARG ASP CYS SER HIS LEU THR SEQRES 22 A 293 MET TRP GLU ASP ARG GLU GLY TYR ASN LYS LEU LEU SER SEQRES 23 A 293 ASP PHE ILE LEU LYS HIS LEU
FORMUL 2 HOH *179(H2 O)
HELIX 1 1 HIS A 42 GLU A 54 5 13 HELIX 2 2 ASP A 73 PHE A 77 5 5 HELIX 3 3 THR A 78 GLY A 95 1 18 HELIX 4 4 SER A 105 GLN A 119 1 15 HELIX 5 5 SER A 133 GLU A 147 1 15 HELIX 6 6 PRO A 149 GLY A 163 1 15 HELIX 7 7 ASN A 167 LEU A 182 1 16 HELIX 8 8 PRO A 189 ARG A 202 1 14 HELIX 9 9 ASN A 203 ASN A 209 1 7 HELIX 10 10 LYS A 228 ILE A 232 5 5 HELIX 11 11 THR A 247 ILE A 258 1 12 HELIX 12 12 LEU A 272 ASP A 277 1 6 HELIX 13 13 ASP A 277 LYS A 291 1 15
SHEET 1 A 8 ILE A 6 VAL A 12 0 SHEET 2 A 8 ILE A 15 CYS A 22 -1 O ILE A 17 N ALA A 10 SHEET 3 A 8 ILE A 56 TYR A 61 -1 O PHE A 60 N LYS A 20 SHEET 4 A 8 ALA A 29 MET A 34 1 N LEU A 31 O LEU A 59 SHEET 5 A 8 VAL A 99 SER A 104 1 O PHE A 100 N MET A 32 SHEET 6 A 8 LEU A 122 SER A 128 1 O SER A 128 N GLY A 103 SHEET 7 A 8 THR A 236 GLY A 241 1 O THR A 239 N VAL A 127 SHEET 8 A 8 GLU A 262 PHE A 266 1 O GLU A 262 N ILE A 238
SSBOND 1 CYS A 5 CYS A 22 1555 1555 2.04
CISPEP 1 GLY A 37 PRO A 38 0 -1.08
CRYST1 54.961 57.095 82.274 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 0.018195 0.000000 0.000000 0.00000
SCALE2 0.000000 0.017515 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012155 0.00000